Sure, but I think I figured it out. After I changed the freighter's "Reactions to events" to "Use Global Settings" the option returned. When I switched it back to manual settings, then it went back to not being there. So it seems to be connected though it may be linked to one of the mods conflicting.
List of mods:
AutoTraderOptions
CAS - community-created gamestarts (Installed but haven't actually used one of these starts Used the original tutorial start)
Collect Inv Wares
fix bail chance
Fix Illegal Buy
Improved Explore Behavior
More NPC
More Chaff
PHQ Warp
Various NPCs