The vinyl really should come out. It has to if it is cushion backed. If it has wax on it the thinset wont adhere properly and the tile will come loose. It may be hiding small cracks in the slab that can transmit upward to the tile causing it to crack in the future. The vinyl can shrink over time causing movement that can be deadly to the tile. The vinyl in my brother's house shrunk 3 to 4 inches over about 7 years. Some say vinyl is a good slip sheet but the fact that it does move and shrink, the fact that it was not designed to be a slip sheet and the fact that it is not constructed to be a slip sheet makes it not a good slip sheet. Period.