If you are using lot of set back and a long stem to compensate for a top tube that is too short is does sound like a bad idea. Your seat position should be based on reference to the crank position which has nothing to do with top tube length and would be the same whatever the frame size.
If you are using lot of set back and a long stem to compensate for a top tube that is too short is does sound like a bad idea. Your seat position should be based on reference to the crank position which has nothing to do with top tube length and would be the same whatever the frame size.