After a few days of troubleshooting, I've found the following conflicts with Watchtower:
Stroud Premium Edition - New Atlantis assets fail to load, crash around 70% of the time when traveling there
Crew Eats - some kind of script conflict
Crew assignments - Not sure, disabled due to crew interactions features
Billboards and posters - crash on Kreet in the research facility and in New Atlantis
running a couple hundred mods, mostly related to adding ship parts, outpost parts, guns, and spacesuits. A number of gameplay mods related to NPC performance, QOL features, and immersion (mining, economy, TN series, and Dark Universe series). Currently running Watchtower last in my load order and have not officially started the questline as this is a new game load and I haven't been able to get further than starting the constellation and UC questlines with this troubleshooting effort.
this is my current load order, with everything now working as it should.
# This file was automatically generated by Vortex. Do not edit this file.
*sfta01.esm
*sfbgs00c.esm
*kgcdoom.esm
*sfbgs019.esm
*sfbgs021.esm
*sfbgs023.esm
*StarfieldCommunityPatch.esm
*WheredtheLightsgo.esm
*Wicked Outpost Projeckt 2.esm
*Wicked Outpost Fortified.esm
*TNClassM.esm
*ShadowFX - Fruit, vegetable, and beer crates.esm
*ShopkeeperSchedules.esm
*sksfderek.esm
*GRiNDTerraverseProcGenBuildings.esm
*GRiNDTerraverseProcGenBuildingsEncounters.esm
*bards_outpostrecruitmentbeaconaf.esm
*ShipBuilderCategories.esm
*TNSpaceMining.esm
*BetterShipPartFlips.esm
*TNUsefulShipStructure.esm
*BSPF-TNUsefulShipStructure-Patch.esm
*TNExpandedCargoHolds.esm
*BSPF-TNExpandedCargoHolds-Patch.esm
*rbt_CaptainsChoice.esm
*TNHabTweaks.esm
*ShipHabOverhaul.esm
*Starfield Extended - Rolling Deep.esm
*golovaliantskilloverhaul.esm
*Starfield Extended - Craftable Quality.esm
*Starfield Extended - Craftable Quality Extended.esm
*WeaponBalanceRevised.esm
*Missing Weapon Quality Tiers.esm
*_vTZvCore.esm
*RebalancedWeaponLegendaries.esm
*TNProperOxygen.esm
*TN_Oxygen_Tanks_Patch.esm
*onek_ships.esm
*useful mess halls.esm
*Gtech Habs.esm
*Habz_HopeTech.esm
*Habz_Stroud.esm
*Habz.esm
*habz infirmary patch.esm
*tnoutintheblackness.esm
*OutInTheBlackness-ShipRecovery.esm
*VanguardAutomata.esm
*AuroraCargoContainers.esm
*immersive slates - ai + cybernetics.esm
*pilotassistantbot.esm
*raijinheavyrevolver.esm
*AtlasClothing.esm
*ODX_Antares.esm
*Starfield Completed - Ship Weapons Matter.esm
*All In One.esm
*AmmoFramework.esm
*M9Bayonet.esm
*PXC_AmmoHud_Patch_M9Bayonet.esm
*AvonTechDeployables.esm
*avontechshipyards.esm
*AUG-Ballistics.esm
*RD_Weapon_Accuracy_Overhaul.esm
*BalancedBallistics_RE.esm
*BetterHarvestingPerkBuffs.esm
*Useful Brigs.esm
*UnleveledShipParts.esm
*PlaceDoorsYourself.esm
*Gtech Habs - Deimos.esm
*MG_ShipWeapons.esm
*MatilijasAerospace.esm
*SETI_ShipLights_by_BosDragon.esm
*RoninCockpit.esm
*ronin useful brigs.esm
*empty1x1habs.esm
*Ship Parts Rebalanced.esm
*EZ_Target_Cspike_CondGrid.esm
*GrafsCockpits.esm
*Infirmary.esm
*Mattells Cockpits Crew Series.esm
*Mattells Cockpits Crew Series UB Patch.esm
*INT_Glassless_Cockpits.esm
*dangerousebbside.esm
*OwlTech_Pathfinder.esm
*OwlTech_Lets_Work_Habs.esm
*OwlTech_Lets_Work_Habs_UB_PATCH.esm
*OwlTech_Ship_Nautilus.esm
*ylr_New1x1ShipsHabs.esm
*kinggathcreations_spaceship.esm
*du_takeover.esm
*OwlTech_Habs_Ship_Living.esm
*forgottenfrontierspoi2.esm
*beltstandalone.esm
*BetterShipPartSnaps.esm
*AvontechTraveller.esm
*Lexingtons_TurretTargetingRadius.esm
*Betterfullautoturret.esm
*BountyHunter_Outfit_Z.esm
*ColorfulClassM.esm
*CoDRipper.esm
*Cosmic_Growth.esm
*rbt_costofliving.esm
*rbt_CostOfSpacing.esm
*CrewSkillOverhaul.esm
*Junk2Resources.esm
*Binoculars.esm
*du_xfire.esm
*du_overtime.esm
*DecorativeEngines_Enhanced.esm
*TNTextilePerkRestored.esm
*EAA_Spacesuits_Just_Work.esm
*DisplayStuffGC01.esm
*Samantha Says - Dynamic Medical Bill.esm
*realfuel_creations.esm
*Samantha Says - Dynamic Repair Bill.esm
*ProjectWarfare.esm
*Starfield Enhanced - World.esm
*BSDM14.esm
*TNSupplementalThrusters.esm
*EnhancedLandingGears.esm
*EnvironmentalSeal.esm
*foodprinter.esm
*G36CRedux.esm
*Companions take ammo.esm
*GCs_ScopeBlur.esm
*ShipVendorFramework.esm
*ZW_AIO_CombaTech_Dark.esm
*FireFlyEngine.esm
*BASE.esm
*GrafsHabs-Nova1x1.esm
*GrafsHabs-Nova1x1-PDYPatch.esm
*GrafsHabs_Mattell_UBPatch.esm
*GrafsHabs-Nova1x1-UBPatch.esm
*vehiclerhyno2.esm
*Habz_Menu.esm
*HO_ships.esm
*GhostPhantom_Part2.esm
*IW Warfighter.esm
*IntrinityAeroworks.esm
*IncreasedHighlightDistance.esm
*Immersive Digipick.esm
*IncreasedScanDistance.esm
*Immersive Speech.esm
*Aurie_CompanionsLetsTalkLater.esm
*Interstellar Traffic.esm
*Minimum Enemy Level.esm
*GrindyCombat.esm
*Human Damage x5.esm
*Realistic Ragdoll and Force.esm
*LandOnAsteroids.esm
*M67.esm
*LeaveNoWitnesses.esm
*MarkM.esm
*MarkM - Starfield Extended Patch.esm
*MarkMRetexture.esm
*MKETurrets.esm
*Satou_Warthog01.esm
*DK_Believable_Crime_Report_Radius.esm
*TNMeleeWeaponModifications.esm
*Lodecs_WEAP_CustomArmory.esm
*dmLegendaryRecycler.esm
*Lodecs_WEAP_CustomArmory_Patch_CraftableQualityExtendedLMR_LM.esm
*weap_outrora_57.esm
*weap_b320_pistol.esm
*MJOLNIR.esm
*ImmersiveShipBattles.esm
*Matilija PDY patch.esm
*radmech.esm
*Mattells Brig Stuff.esm
*MercHeavy.esm
*MoreInterestingAlienDNAEnhance.esm
*WeaponBalanceRevised - ShatteredSpace.esm
*Missing Weapon Quality Tiers - SS.esm
*EAAMoreSupplyAmounts.esm
*ShopkeeperSchedulesDazra.esm
*Nades.esm
*Nomad_Spacesuit_Z.esm
*OutInTheBlackness-ShipRecoveryFixes.esm
*ObstacleCollisionDamage.esm
*LowerRegistrationFee.esm
*OwlTech_Echoes_Of_The_Past.esm
*OwlTech_Echoes_Of_The_Past_PDY_Ship_Patch.esm
*Mattells Crew Series SETI Patch.esm
*PlayerSpeedRevised.esm
*Starfield Extended - Rolling Deep - TNHabTweaks Patch.esm
*TN Habs Tweaks - Rolling Deep - Ship Combat Overhaul.esm
*ProjectWarfare_SkinPack_OSA.esm
*ProjectWarfareAddonPack1.esm
*x2357primeweaponskinsprojectwarfare.esm
*ProjectWarfareAmmoPatch.esm
*RD_BWQO.esm
*RD_Ecliptic_Overhaul_2.esm
*RD_Ecliptic_AI_Overhaul.esm
*ShipRammingDamage.esm
*RealisticNPCAmmoUsage.esm
*Resupply.esm
*rocksgverseppg.esm
*Ronin Balanced patch.esm
*RotatedEngines.esm
*RotatedShieldGenerators.esm
*Starfield Extended - Craftable Quality - TN's Melee Weapon Modifications Patch.esm
*SN6AdvancedWarfare.esm
*Starfield Extended - Shields Rebalanced.esm
*SOL - Sensible Outpost Lighting.esm
*SeizureOfShips.esm
*Sense_Robots_And_Turrets_Too.esm
*GB_ShipBuilderConfigurator.esm
*ShipColorize.esm
*Sithtrooper.esm
*uc_reuniform.esm
*SVF-Generic-AllShipModulesUnlocked-AllShipVendors-Patch.esm
*SVF-ShatteredSpace-Patch.esm
*SVF-Generic-AllShipModulesUnlocked-AllShipVendors-ShatteredSpace-Patch.esm
*Sit To Add Ship.esm
*PlanetDB.esm
*SmartInventory.esm
*SpaceMining.esm
*Starfield Extended - Reactors Rebalanced.esm
*starfieldfleetexpansion.esm
*StatesOfMatter.esm
*Hal_Sun.esm
*Straw_BossChestsContainLegendary.esm
*TNHabShells.esm
*TNSupplementalReactors.esm
*TN_Textile_ShatteredSpace.esm
*TNWeaponToModuleSnapping.esm
*Timefield_5_10.esm
*UC Surplus Expanded - Immersive.esm
*UNSAClothing.esm
*UnleveledShipParts-ThetaPinchE9Reactor.esm
*ws_VariableContrabandPrices.esm
*yTS-27.esm
*Gtech Habs Useful Brigs patch.esm
*habz pdy patch.esm
*zGrind.esm
*Desolation.esm
*SW Coruscant Guards.esm
*additionalweaponicons.esm
*astrophysicsreworked.esm
*darkerspace.esm
*easy_temples.esm
*elitecrewiselite.esm
*functionaldecor.esm
*g17x.esm
*goloaerobicsskill.esm
*golobeginnersluckskill.esm
*golobloodrushskill.esm
*golocoffeefiendskill.esm
*golokenjutsuskill.esm
*golomomentumskill20.esm
*golosentinelskill.esm
*goloskillchallenges.esm
*gtr-port.esm
*immersivecontraband.esm
*improvedfollowerbehavior.esm
*m4a1assaultrifle.esm
*mad_freestar_grounddefenses.esm
*nk_andrejawalk.esm
*non-lethal framework.esm
*novafinch_enforcerpistol.esm
*overhaul missile behavior.esm
*weap_t77_pistol.esm
*pistol_laredo_m2.esm
*projectwarfare_skinpack_nv4.esm
*rav-8.esm
*sanctum universum overhaul.esm
shipworkshopassignments.esm
*silverhand3516.esm
*sp2_sarahmorgandialogueenhanced.esm
*starfield billboards and posters.esm
*starwarspatroltrooper.esm
*starwarsshoretrooper.esm
*starwarsshoretrooperparadiso.esm
*sw bespin guards.esm
*terrifying terrormorphs.esm
*uc battlemeals adjustment.esm
*vcvas31.esm
*vivs_furnishyourfleet.esm
*w&dsmg.esm
*weap_laredo_m2pistol_rattler.esm
*weap_outrora_aap.esm
*weap_starlight.esm
*RD_Pirate_AI_Overhaul.esm
*spacesuitbalancerevised.esp
*aGTFrame.esm
*oneilstation.esm
*rbt_Roverhaul.esm
*rbt_SpacefaringEconomy.esm
*rbt_SuitUp.esm
*rbt_SuitUp_Enviro.esm
*SFF Body Replacer.esm
*SmartHeal.esm
*TBoBF.esm
*The Mandalorian.esm
