What stops indies from using illegal software to build their games?

I don’t think that’s accurate, without working together the different software companies can’t guarantee that metadata gets passed on between programs. Some formats aren’t designed to have that info, and even then, once it’s imported to another program it would have to keep that info so it can pass it on. Take .obj for example, even if it contained metadata, it’d be very easy to make a program that ignores that info. Now, if you’re using 3ds Max/Maya directly to UE4 using FBX then it could very easily work with that kind of metadata, but otherwise it’s very easy to get around if it exists.