How does this work, exactly?

Those are all excellent questions that I, too, do not have enough law-school education to answer correctly.

I can take a vague stab at some of them, maybe, by pointing out that the exact boundaries of what is and is not patent infringement is likely to be decided by a judge (or de facto decided by the lawyers who evaluate legal risk, at least). So while there may not be much of a _technical_ difference between Fedora letting uses add RPM Fusion repositories manually versus having a button to do it, it still seems likely to me that there's enough of a _practical_ difference that it could sway a judge.

The fact that these things are decided by judges, who are human, using their best judgement also means that there may not even be a hard-and-fast rule for what is or is not acceptable until someone has a precedent-setting lawsuit about it.