My thought is that unless the vinal is cushioned, it should be okay. The toilet needs to be solid and not rock. If the stuff you put under there is a little undercut so there is room for a bead of caulk, I think you should be okay. Otherwise, it would be tough to make it look good. Is the bottom of the flange flush with the top of the finished flooring? If it is, and the toilet doesn't fit, how high (thick) is it? Just curious as to why it doesn't fit.