Can you just rough up the vynal and thinset on top, or do you have to put down a underlayment such as durrarock or hardiboard? This would be in an existing bathroom.

Roughing up the vinyl would be harder then just ripping it out, IMO. Do it properly the first time and you won't have problems after.

Tickle said it. You want a permanent installation, go with 1/4" hardibacker and then tile. Set the new threshold on old floor and butt up to that with the 1/4" hardibacker board (tape seams and use their screws and screwbit) and then tile.. threshold hides transition to hallway or bedroom.

This leaves the toilet flange 1/2" below the finished floor so will need to purchase a toilet flange extender kit and an extra thick toilet wax gasket to install the toilet correctly.

Get back to us if you have any questions. Take care... MARK