Eh, I dunno. Upon a second read, I may have jumped to conclusions a little too quickly. I fully admit I'm biased toward William's side, since afaik he worked on this project for a while, and was only told *after* it was ready for implementation that it would not be added to the game.
Personally I think it makes quite sense.
1) Pirates absolutely attack goverment people (doesn't Black Void pretty much mess around on Myrellion in their base?) and the first thing that happens to you is getting jumped on Zheng Shi even if you try faking as a pirate (unless you intentionally piss them off them the Korgonne wisely decides to not piss you off)
2) seems bit iffy i do kind of agree with nonesuch. but doesn't Black Void pretty much have entire black site research stuff? doesn't seem unlikely for Sophora to be pretty much redacted biologically since she seems to be rather influent, or a complete utter genetic mess (especially since she does have some rather odd quirks)
3) You literally have the option to get rid of her on first encounter, the reasoning of letting her just leave and live is because Captain Steele is curious and wants to fuck around (literally) and find out, Kind Steele can outright try to kill her when Sophora beats and abuses them, but doesn't because kind while she gets the memo that she
WILL die if she shows her face again.
What's the issue? yes i do agree some things of Sophora were bit too wild but fuck the entire game is literally "unexplored wacky and crazy planets with crazy people" I think it they absolutely screwed over Will, especially since it was literally all finished and only then they went "nuh uh, this is no bueno!"