I have only used boiling water and it usually works quite well. I like a good boil, but not the most rolling. It seems when I use the full rolling boil, the end caps (if there are any) pull away from the seal, probably because of the extra steam created by the higher temps. When that happens I figure either the boil is too great or I need to leave it in just a little less.
I suspect the dimpling effect some have experienced is due to that particular brand of seal. I would try other brands if I could not get a good smooth seal after dipping. Maybe some seals are better to use with a heat gun and others are fine to use boiling water.
My technique is to hold the seal on the inverted bottle with the handle of a long wooden spoon, dip the bottle into the boiling water for no more than 1-2 seconds, giving a slight twirl while it is immersed (that seems to equalize the shrinking effect) & quickly remove & dry. I keep the bottle at an angle, not straight up, because I don't want my hands over the steam.
NS