All very interesting. Never put water in a tire myself, so it's clear I do not know what I'm talking about. But, if the tire is indeed full of water above the stem when the stem is at 12 o'clock, it may very well be that the water won't come out on its own, especially if the tire/wheel is jacked up off the ground (it may even make sense NOT to jack it up so that the weight of the tractor etc. will help in pushing the water out).
Did you ever change the heating element in a hot water heater without draining any water at all? Just make sure that all the faucets are shut so no air gets in, then gently remove the old one, and carefully slide in the new one.
I'm guessing that if the tire is full of water, something has to help in getting air in so that water can come out - maybe do as Bird says - remove the core - then get a cocktail straw or something like a IV cathater to get air in.
Or, maybe it's really no big deal, I said I never had a tire with water in it, didn't I?