A good caulk person can lay a bead that will look finished. Most of the rest of us smooth it after application. I doubt there is any reason not to if it is not perfect out of the tube. I've been caulking counters for over 25 years and am not of the chosen ones that lay it down perfectly out of the tube. I smooth it with my finger and always have a bucket of water with a rag on the bottom to keep my finger wet and clean.
Sounds like these guys are plumbers not finishers
I try to put as little caulk as possible. Cut the tube with a very small hole and generally you don't even see my caulk lines. If the counters fit correctly there will only be a minute line of caulk when I'm done. Just enough to make the seal. This all depends on several factors. Mostly fit.