If the value of the original ticket was recovered by payment of a no show fee and change fee plus fare difference then by mymy understanding the unused APD would have been put towards the replacement ticket and hence no APD refund would be due.
However if a completely new ticket was purchased on a new PNR then there is probably some APD available for refund, but that will be subject to any fees leveraged by the travel agent who booked the ticket and has to administer the refund. Their costs would have been called out in their T&C's which I assume were accepted by the OP when booking. You will need to accept that £55 admin fee or give up.
As the OP ended up getting a new passport issued, the denied boarding angle is now very weak. The only possible path in my opinion would be to get a written statement from the Thai Embassy stating whether the blank page would have been acceptable for entry into Thailand by immigration (note: it's immigration not customs as discussed above). If the OP can be bothered to go through that they then potentially have a good case to pursue QR for denied boarding compensation at €600. In which case come back here and ask for more advice. The British Airways forum has a good thread that offers advice on EU261 claims which would be a good read for the OP, but as the query does not relate to BA don't post questions in that thread but come back here.
Good luck.