Caulk is not really what seals those seams- it is there as a line of defense if the butyl fails.
That said, I don't have anything against a good quality RTV silicone on the sidewalls- I have 20 year old silicone caulk jobs I've done still in good shape, but... the caulk I used isn't carried at normal stores, the closest is Permatex RTV silicone- ~$13/tube. It has good adhesion and is very flexible (low modulus).
Yeah, it must be completely removed if it needs to be replaced, but if applied correctly it won't need to be replaced, and it is *way* easier to remove than Proflex.