Is it safe/wise to run tires slightly overinflated? I commute 10 miles a day on an '11 Trek Allant with the stock tires (700x35, Bontrager Select Invert I think), and the recommended PSI range is 65-80. Ever since I got a snakebite on the rear, I've been running at about 90-100PSI for a little peace-of-mind (I'm 290).
I've also been noticing a little brake drag on the rear; do you think the overpressure is deforming the rim enough, or is that an alignment problem?
It is probably an alignment problem. Nonetheless running a tyre with an 80psi max at 100psi is not a terribly clever idea. Slight overinflation is safe enough, but to overinflate by 25%, as you are doing, risks the tyre blowing off the rim at some point, most likely under hard cornering. I wouldn't do it if I were you.
If you are worried about pinch flats, get a slightly bigger tyre. Though with a 35mm I'd say you were unlucky to get one at 80psi.
The brake drag may be an out of true wheel.
I run my tires just under 10% their "maximum" recommended pressure.
Pinch flats are as often due to the tube getting caught between the tire and the rim when it was installed or grossly under inflated. A properly installed tube in a properly seated tire shouldn't get a pinch flat anywhere near the max psi.
As has been discussed also in this forum, big folks can help themselves out by learning to ride "lightly." This is simply to get a feel for bumps and gently lift weight off the seat, allow the frame to pivot around the crank arms, or stand up on the pedals and shift dynamically the weight forward and back a little to allow the bike to ride over rough terrain. This can drastically reduce shock on the wheels and rims.
I ride 700x28c tires at 80 psi Front/90 psi rear (rated for 87 psi) and 700x32c at 55psi F/65 psi R (70psi max). I can't say I've gotten a pinch flat in more than 20 years. But I guess there's always a first after this long. I weigh around 280lbs.