I'm not sure if this is suppose to be a problem but I'll share this just in case:
Long story short, due to the file descriptions here and at filefront, I'm under the impression that I can choose what hilt I can use during the last stage of the saber crafting quest and when asking Bao-dur to make more sabers later. That wasn't the case apparently when I reached that part of the game since I can only choose standard crystals during crafting which instantly gives me default sabers afterwards.
I can't say that mine is broken though since Kreia has the walking stick, I'm still getting the USM crystals in loots and placing them in existing sabers when using the workbench does give me unique hilts, and the workshop/lab terminal in dantooine runs properly.
So I don't really know what to say, honestly. Am I missing something here or are things really working out properly?
I'm still not sure about the part where I can make my companions craft their own sabers though since I haven't reached that yet.