I don't think the Dynaflow would bother me as much as the subframe. Who knows how well it was installed; you'd probably be in for more problems as a result of that than you would be in regards to the transmission. There are enough stock '53 Buicks for sale out there that I would hold out for one that hasn't been modified (unless that's what you want).
With that being said, there's no way you'll be happy with this car if you expect it to have modern performance. I regularly drive slow cars in traffic (Corvair, slant six Dart, '53 Buick with a straight eight and Dynaflow), but I live in a middle-sized Midwestern town with no hills. My Special keeps up OK with the Dynaflow (that has less power than the Super), but there's no doubt I'm using more pedal than I would have back in 1953. People in traffic see you as a rolling chicane these days if you're even driving the speed limit, so you'll be pushing the car harder than you might want to if you're using it as a regular commuter. And of course your mileage will suffer as a result if that matters to you.
So, as many have said, a '53 Super is certainly capable of being a daily driver, but there are some drawbacks to doing so. The fact that you have experience in a Dynaflow car and are this unsure if you want to repeat it seems to answer your question for you (IMO). Maybe a good compromise would be to find a '53 that has been upgraded to a later Buick powertrain.