I’m just going to say that this topic feels very…grey area. That said, I’ll answer your questions:
What stops indies from using illegal software to build their games?
The security protection, hopefully. If that doesn’t, then your morals. If that doesn’t, then nothing.
Can somebody explain those things for me?
Almost every software has different subscriptions/licenses these days. The one i’m most common with is the “buy one for each computer that will be using it” type. This is why game development can be costly. Four maya licenses add up.
I’m not sure what you mean about registering a studio with a game. If you created the game, you include your information, such as “Copyright of Mycompany, LLC” in it. That honestly should be enough, but when using the unreal engine, a tad more has to be included to protect Epic as well. If you made a project/game, it’s yours, as simple as that.
If you have more questions, I’m glad to help out!