i didn't notice that the braze-ons aren't symmetrical. Which frame are you riding? I believe that the seat stays on the Comp are different than the Sport for instance but i'd be surprised if they weren't correctly placed. When I get home tonight i'll try to put a picture or two up of my TriCross Comp with the Topeak Explorer rack on it.
As far as i can tell most every rack (and definitely the 3 that i've tried) have 2 physically attachments at the seat stay (left and right) and it's definitely possible to install it in a way where it's not even. I always use a level on the rack to place it left to right and back and forth and some blue thread-lock on the bolts. Torqued properly i've never had one move. (torqued improperly i've had them move around a lot so i'm kind of anal about it now
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I do not have fenders so i can't be of any help there.
As far as heel strike i wear a size 12US, i think that's a 47 or 48 in the rest of the world. I've found that carrying a large set of panniers on a "standard" rack is impossible for me. I need a rack that sets the panniers back a decent amount. The Jandd Expedition works, the Topeak Super Tourist works (although that one's pretty impossible to find in the US and the Tubus would work. Because the rack pannier is set back pretty far the rack really needs that additional dogleg shape that keeps the pannier off the wheel - if you have that you shouldn't have an issue.