You can still hike the PCT with out a PCTA issued permit, you just have to apply for permits from which ever land authority you are going to be passing through.
The PCTA permit was done so that thru hikers didnt have to go through the hassle of applying for the numerous permits that would be needed.
The PCTA cant stop you hiking and dont have any authority in regard to you hiking. They are just there trying to help hikers with the process.
The other way to do it is do a flip flop hike and get your permit starting somewhere up the trail, there usually isnt an issue getting one of those from PCTA or do a SOBO.
I did the AT in '14; first 400ks of the PCT in '15 and the rest of it in '16( that is how I know about the getting a permit starting up the trail)