So two things to consider, acceleration from stopped, and top end speed. And based on your question, the following are identical:
- Engine horsepower
- Gear ratios
- Tire size
And the only difference is one is a transverse mounted front wheel drive, and the other is a rear wheel drive.
Acceleration from a stop
In this case I think if the two cars have enough horsepower to break the tires loose so they are slipping rather than driving the car forward (doing a burnout), then the RWD would have some advantage. That's due to the weight transfer mentioned by @DucatiKiller in the above comment allowing more horsepower to be applied to the tires without breaking them loose.
For the top end, it's a question of force applied to drive the car forward vs drag. But, there is one more thing that's different between the two. The transverse mounted FWD has a much shorter drive train than the RWD. Same components ultimately (transmission and a differential) just no long drive shaft. Honestly, the amount of energy lost in heating up the longer drive train when compared to the FWD shorter path is negligible compared to the losses in aerodynamic drag. So if I had to bet, the FWD would technically be faster by an amount to small to be measured or matter.