Also I read somewhere that it will not allow flight in permit aircraft
That is not entirely true. 'Permit' aircraft fall into Annex II of the Basic Regulation, which lists aircraft that are administered by individual states. EASA cannot, for this reason, introduce any legislation (including licensing legislation) that affects Annex II aircraft and the Implementing Rules do not cover them. However, each individual state will have to produce requirements for pilots to fly Annex II aircraft on it's registry and it is logical to suppose that they will use to the EASA licensing system - we just don't yet know how this will be done.