I may be wrong, but I think the PFA wanted the Salary Cap scrapped as 'unlawful and unenforceable', but they only succeeded in having is stopped on the basis of improperly followed protocol (e.g. due process consultation). If this is correct (and consulting is the same as that carried out during redundancies i.e. the PFA have the right to put alternative proposals that have to be considered, but ultimately don't have to be agreed to for the changes to be implemented) then if the EFL undertake the correct protocol they can still impose the Salary Cap, regardless of whether the PFA agree or not.
I think the most important factor may be that the judgement does not alter the inability of the majority of clubs in L1 & L2 to afford to pay players any more than they are currently paying and some are thought to be incapable of even paying that. This will inevitably leave Sunderland, Ipswich, Charlton, Portsmouth and the like railing against the rest of us for some months yet.