Caulk is a horrible idea, and a code requirement in my area. If you are on a wooden floor system (floor joists and plywood sheathing) and you have even a slight leak in the base to wax ring connection, the damage is nicely concealed by the caulk. I have seen several cases where the bowl was caulked to a vinyl sheet floor, and the owner complained that the toilet "rocks". It was rocking for a good reason. The ring was leaking for years, the plywood floor has turned to mulch, and there is one hell of a repair bill about to be paid. I had one job where we had to pull the toilet and vanity. Cut all the subfloor out of a small bathroom and replace it, since the toilet leak had destroyed much of it. The job was a bit stressful, since it was the only bath in the home, and it needed to be completed in one day. Had the homeowners noticed a slight leak at the base of the bowl, years before, it would of been a quick, easy repair to install a new wax ring. Instead it was ugly and expensive.
As for caulking to further secure a bowl that's rocking? That's a bad idea. There are several repair parts and work arounds available for flanges that are in bad shape. If you don't have the ability to securely install the two closet bolts to a usable floor flange, don't half ass it by trying to bed the bowl in caulk. You are only creating a bigger mess down the road.
