I have an Enco 12" RT more or less permanently mounted on my old mill drill (at 200 lbs., I don't like to move it). The center hole is cylindrical and 1" in diameter. I made an adapter for the 4" chuck from my Atlas/Craftsman 6 x 18 (it has a 1"-10 tpi spindle mount) which is threaded into a backing plate on the bottom of the RT with a stud from my clamp set. This makes for a quick centering fixture for cylindrical stock.
To reference the RT, I will put a piece of stock in the chuck and and make a cylindrical cut on the stock by offsetting the RT slightly and rotating the RT through 360º while cutting with the end mill. This creates a cylinder which is centered on the RT. I then use my edge finder to find the center of the boss (left side,right side, front and back) and set my mill DRO to 0,0. For larger work pieces, I remove the chuck and use the edge finder to find the center hole in the RT.