Tricky situation
The fuel door on my car was a pain in ass to disassemble, I was however able to remove the orginal boot, then reassemble it with out the boot. I will be refilling the tank now through the trunk. I did the same thing on my 71 2002, it just keeps gas where it's supposed to be in the tank. As far as a flush fit my fuel door is good fit, possible yours is damaged, bent hinge maybe? My 2002 would always leaked gas all over the paint with a full tank, so I got a filler neck from some other BMW can't remember which one, but the neck on the coupe looks similar to the one I retro fitted to my 2002 has nice tight cap. I'll be leaving the coupe the same way even after the paint is done it also doubles as a locking gas cap also!