The "good faith" breach only applies to the filing incorrect accounts allegations (also to non-cooperation after 2018). So I think what they are trying to say is that Mancini's consultancy agreement was clearly part of Mancini's salary and should have been included in the club's accounts. Because it wasn't, the accounts were wrong. It's pretty hard to prove that, I think, for a whole host of reasons and, in that case, the whole thing will probably be time limited anyway.
The breaches in respect of the manager remuneration rules (or the player remuneration rules for that matter) don't refer to the "good faith" breach so will probably just be a procedural issue with the PL. Did we comply with the rules as written? And I think the answer to that is clearly yes, especially after the Leicester judgment.
I think that's the situation, although it could all be bollocks :)