Is there an issue with that? As long as all parties agree and it’s in writing, it just sounds like another of the many clauses that are added into contracts.
As far as the authorities are concerned, yes. Never used to be, I remember United and Newcastle mutually agreeing not to use either Andy Cole or Keith Gillespie when we met in the next match following their respective transfers.
Not sure, but it might have come in after the Tevez/Mascherano thing and a further tightening of the third-party ownership rule. Either that or something to do with the rule over people supposedly not allowed to own more than one club. I suppose if someone other than the club who now owns the registration of a player is telling that club they can't pick them then it's an outside party having influence over the player or club. It's strict interpretation of the rule, no doubt, as this kind of thing has always been done but I think that's what they wanted in order to clear up any grey areas.
Of course, the daft thing is you can still do it just as long as you don't say you are. Just say the player had a slight knock, hadn't had time to train yet as he was busy moving house or hadn't integrated well enough with the squad yet so you're leaving him out if asked. Something like that would do fine.