Let's just go through the extreme logical end to a "permissions" fight.
Here's where things start to get stupid.
"Permissions" restrictions are only worth the legal might behind them. Until someone's actually willing to go to court over a free mod they essentially lose money on developing in their free time as a hobby, permissions mean nothing.
And that's all assuming they're both US-based entities. If we're discussing international conflict that's a whole hell of a lot messier.
There's also the legal quagmire of most of these mod authors fucking up their EULA agreements so that they're not actually legally binding and probably wouldn't even end up being material to the case in question.
(I've often fantasized about diving back in to Java and making a mod, just so I could slip some obscure agreement into a correctly-done legally-binding EULA that says something along the lines of "the author of GregTech and any mod author that professes to deny permission to distribute/modify any Minecraft-based work they've produced may not download or use this mod", and then just have code inside it that monitors for known authors who would be in violation of that EULA using the mod in question.)