I offer apologies, and will appeal to Sith Holocron (as he knows me to do )
It's not that we aren't open to intellectual discussions (as you say) about the game, it's more that these points have been discussed already, seem pretty open and shut. I too am guilty of doing this same thing in the past, telling newcomers to shut it. We all make mistakes
As the main developer/contributor/restorer of the TSLRCM version of the HK Factory, I'm happy to engage in discussion as to what was done and why.
The poison gas mines were present in the original files (salvaged from the Xbox version of the game) and I left them in as part of it, since as Darth Parametric noted, the HK's remark that they had prepared the base for defense against organics. It speaks to their arrogance that they didn't even consider that an HK unit could have infiltrated their base.
That was my analysis of the lines, and it contributed to keeping that in.
As far as why Bao-Dur's ending was not implemented, it's partially due to there not being enough content to produce the original ending. Bao-Dur was supposed to help HK get to the Telos base, and die on the way, but due to a lack of VO, it's hard to make this ending a reality without seeming out of place (in my opinion at least).
There have been ideas on different ways to close out Bao-Dur's story in a meaningful way, a thread somewhere on the forum here. IMO figuring out how to give Bao-Dur a meaningful death with the available dialog is a better use of discussion, rather than trying to discern details of the HK factory.