Any suggestions for properly countersinking a hole for re-bedding a through the hull fitting? How deep, based on the existing hole thickness (deck thickness) and how much of an oversize (diameter) would be best? In the past I have had issue with the drill bit being drawn in causing the countersink hole to be too deep.

I've used a piece of PVC pipe as a sleeve around the drill bit to act as a back stop so I would not drill too deep. I'm guessing there are better methods.
Ther is no real need on thru-hulls. Thru-hulls, like genny track, has a concave channel on the back side of the head to catch and retain marine sealant.
When countersinking use your drill in reverse if your countersink bit is still too sharp. Some countersink bits have a hex head and can be put into a screw driver so you can do it manually. I usually just dull mine in some SS before using it on gelcoat. I keep the old dull ones for use in soft wood or gelcoat.
If you still feel it necessary to countersink for a thru-hull use a laminate trimmer with a 45 degree chamfer bit that has bearing guide. You only need to soften the edge slightly.
Oh and do not use butyl for below water applications. Use Sika 291, 3M 4200 or a polysulfide.
Keep in mind that the hole in the hull should not be over-sized for the thru-hull and should be a nice tight fit.
This shows where the sealant sits to make the seal.