Is there a difference between a RS auto and a WRX
auto? I'm just wondering if my RS auto could handle
a WRX motor swap.

The torque distribution system is completly different. The RS uses the system that subaru has used for years, while the WRX uses a system like the VDC or STI 6 speed. Otherwise besides gearing they should be equal.

As far as handling power I dont think a difference exists.