When we first adopted Peppy, her teeth were misaligned…like you mentioned, her bottom teeth were overlapping her top teeth a bit. Because she was still young, and because her teeth were so very close to being normally aligned, the vet said that if we were lucky and kept doing the trims, they might grow back correctly some day. I guess things did turn out pretty well, because just a few trims later I checked her teeth one day and they were normal looking! Apparently it doesn’t spontaneously resolve like this very often, and we got pretty lucky. It probably helped that we discovered the problem and started the trims when she was quite young too.
Milo on the other hand…when the shelter picked him up, his teeth were already so severely overgrown that he could hardly eat. They tried trimming for a while, and after it became clear that his teeth would never align correctly, they just went ahead and had his incisors removed (this was all done before we adopted him).
I don’t think the tooth trimming should be too uncomfortable…they usually put the buns under anesthesia just for a little bit to do the procedure. I’d even say that Peppy was happier after her trim…when she first came home I realized she avoided very crunchy foods and had a weak bite, though I didn’t know why at the moment. After the trims she started eating better; I’d say that it made her feel more comfortable. Keep us updated with Sugar’s teeth!