One of the major reasons for engaging the PTO with the deck up is to keep the PTO belt at an easier angle for the equipment. With the deck down, the belt is more steeply angled into the deck drive sheave making the belt vulnerable to jumping out of the sheave on start-up. It happened a couple of times on my 2544 when it was newer. You'll put a nice gash in the belt when it happens. Even with those, I'm still on the same PTO belt! ~4yrs and 120hrs. You know it will break on my next mowing.
Joel