Ever since the dialog.tlk was included this has already been adjusted (by a simple .tlk tweak, no .uti needed).
Apparently... no one noticed.
Seems to fix HK to Evil... AFAIK only Kreia should have a fixed alignment.
Gives the party the same XP as the PC. Again, not exactly what was intended... :/
As others also stated, it was made this way for convenience... which makes it intentional. I can understand the canon-people wanting a canon setup though, for them there is the mod.
Nope.
No. That's the way the game works after Dantooine's meeting. It's also set up to erase data from NS/Dxun/Dantooine and Korriban upon the Telos battle. Altering the .2da that does that could work (never tested), though is it really needed?
Yes, you need to travel to the Unknown planet in KOTOR, but you also need to travel to the Jedi Masters on Dantooine in KOTOR2.