Alas, I fear you're probably correct, even though (in my view) it would illogical to treat them differently, given the EFL rule is nothing to do with the FA. Hence why Bielsa also faced with the same "disrepute" charge, surely?
In other words, if a pre-requisite of the FA being able to accuse a manager of "bringing the game into disrepute" is the pre-existence of a rule they've broken in whichever league they happen to be managing in, then how were they able to bring a disrepute charge against Bielsa in the first place?
(On reflection, I guess the answer to this is that he was in breach of the lesser EFL 'general misconduct' rule, which pre-dated the spying rule... Bugger... Just blown my own argument out of the water... Probably... )