is it possible to resurface the end cap by taking off a few thousandths of metal using 400/600/800 grit over glass?
hydrostatic transmissions are not all that complex, you can't have huge scoring on surfaces resulting in pumping leakage after that it's basically cleanliness and no case seal or shaft leaks and controlling oil temperature. For that reason I would argue a buna (nitrile) material is a better choice than viton- you generally do not "need" viton if you maintain oil temperatures. That's like saying I need "synthetic" engine oil because it runs hot.... no either you need an oil cooler or reduce the load on the motor/transmission to manage the heat. The engineering behind mower hydro mower transmissions is pathetic, no thought put into cooling = overheat = duh let's use viton that'll fix it = disposable mower because of oil overheat lubrication failure which is the real problem.
if u end up fixing it and changing nothing else, then I would use a viton seal to "help" cope with the high oil temperature since you already know it will likely get hot. but that's kind of like a bandaid on an underlying problem, you should try to incorporate some kind of cooler (power steering cooler does not need to be complicated). hydraulics (transmission, hydrostatic trans, power steering) is all fundamentally similar.