its probable the joints in the boards as to why they want to ply it just tell them to use ardex feather finish that will sort the bad joints and is only half a mm thick and shouldnt pose a problem to your bath panel if the joints are fine and theres only slight movement sand the joints and lay...
The yes this is a tricky job , wat i do is cut under one side and round the arcatrave on the other side and finish with the same colour seal you can get it from b&q this will leave enough room on the other side for expansion hope this is a help :)