As long as you have the "working day" be based on rests rather than a planetary day it shouldn't be a problem. The rate of encounters changing with a short rest is just changing the overall pace of the game.
Mostly. You may or may not want to blacklist a few combos - like a Mountain Dwarf Wizard starting with Heavily Armored? Or some Variant Human wombo-combos, like taking both Crossbow Mastery and Sharpshooter at 1?