I bought a used pair off eBay also about a year + ago and noticed this also...the top of the fuel door just barely "kisses" the side rack when opened
My solution...was to be slightly more careful when opening the fuel door and putting an ever so light down pressure
when opening the fuel door...the slightest pressure was all it took...over the last year or so the fuel door seems to have "realigned" itself so that the down pressure is not needed anymore
Since I'm a bit of a klutz
I also put a thin strip of clear "decal like" vinyl over the top of the fuel door at the rub point...just in case I forgot
I know that I installed correctly...I had KiwiDave send me all the new correct fittings etc...I just figured that the previous owner had too heavy of a bag or something attached to the side case rack that slightly distorted it.
I only paid $50 delivered for my nearly new KiwiDave pair
so I was willing to tolerate the slight inconvenience, that went away by itself anyways
You are much more knowledgeable than I am regarding forces etc....so if you come up with a more elegant solution send me a PM.