Nexus does not list any specific rules about this as far as I can tell, but Covers should be fine so long as they do not contain any samples, vocals, or other components of the original piece. You should also look more in to what the companies that own the content you want to include in your mod have to say than the nexus itself. Konami is one example of a company that's pretty open about their content being used in non-profit derivative works, and if it's cool with them, it's cool with the nexus.
Not that it really matters, but that's how Newgrounds handles things, and they take Copyright much more seriously than the nexus when it comes to enforcement. (Any existing uploads on the nexus that seem to violate these rules exist as a failure of moderation, rather than a sign that content is allowed.)
Edited by Radioactivelad, 11 September 2022 - 01:20 pm.