without photos, if its truly 1mm clearance, as you say yourself, its just too bloody close. I'd size down going from your own accounts of same bike/clearance.
do take into account the possibility of maybe dremeling out the fender top mount thingee, to bring the fender up a smidge, or even dremeling out some of the fender itself, to allow you to bring it further up. Ive seen someone here post photos of doing this, but having to add two mounts at the fork area, essentially splitting the front fender into two parts--but to me this is a lot of work, just go with slightly smaller tires like the 35 or 32s...
I put 32s regular marathons on an old trek hybrid with fenders and as you say about stuff getting stuck inbetween, it can happen and at a certain point you have to use common sense and just go with smaller tires (unless you go the "split fender in two" route, which is a bit complicated)
Yeah...i am not against cutting into the fenders around the crown to raise them up and then re-enforcing around that are if need be. I just dont want to do it if i dont have to. I dont have fenders yet and want to find some used so i wont feel so bad if i have to chop them up.