Even if KotOR Tool doesn't locate your game in the registry, you should still be able to set the games path manually.
And actually, I don't think the bundle version actually creates a registry key, which is weird. It didn't for me, anyway. Try adding the key manually.
Failing that, there is a piece of software called KISS that will allow you to unpack .bif files. I don't have a link, so you'll have to do some googling to find it, unless anyone else who drops by the thread can provide you with one.