You could overinflate a pound or two to make sure you are at the right pressure once you have released the pump. Afterall tire inflation is not a super precise part of the bike. I would guess the small pop and whoosh is mostly air from the hose, but its easy to compensate.

The nut should be snug enough to hold the valve in place, but it doesn't need to be more than finger tight for that purpose. Remember as you inflate the tube you'll pull the nut down tight against the rim. If you get it too tight its a PITA to loosen when you get a flat and have to pull the tube.