My broad recollection is that the basis for this is that the Phoenix is required to operate a youth/reserves team under the A-League license T&Cs, and NZFs position is broadly that there will be better opportunities for NZ youngsters in a team based in NZ, rather than Australia. Right now the A-League agree that Reserves in NL fulfills the obligation.
I was at first opposed to the automatic entry, but on balance and after some thought, it does make sense for NZF to agree to this, if we wish to retain the Phoenix in the A-League- perhaps that is the lens to see it through - better on balance for the Football ecosystem in NZ that the youth team operates here than in Oz, comprised mostly of Australian youth players.