I’m still a bit lost on what happened. Is it as simple as FIA investigates the Ferrari PU for cheating, Ferrari disagrees, then settlement reached without any clarification of what happened?
If so, is it possible the FIA didn’t disclose what they did because there could be IP being disclosed to the public? Is there any precedence to this?
The suspicion I've read the most is that they've figured out a cheat around fuel flow rate monitoring/sensors. F1 regulates both fuel used overall and the rate burned. If you remember, Ferrari's straight line speed advantage disappeared at the end of last season. That was right about the time F1 issued a Technical Directive at the request by Red Bull who asked if something altering the fuel flow sensor intervals would be legal.
F1 shares with all teams anything asked by a team that is determined illegal. If a team asks for something declared legal, F1 allows it and doesn't share it since it's IP. Like Merc's steering this year.
In this case, it looks like F1 thinks Ferrari is cheating, can't prove it and decided to do whatever extra monitoring is necessary/got Ferrari to promise to not do whatever it is they think they were doing. And then not tell anyone.
If you're confused, it's because F1 is trying to play the middle and not piss off Ferrari. I mean something is either legal or it's not. If it's legal, they can keep it secret. If it's illegal, they supposed to reveal that to the teams. All non Ferrari teams have every right to be upset.