Sorry for taking so long to reply, I finally had some free time to spend on DCS.
You are correct, even with the RPM reduction from the RATS, the speedbrakes are supposed to retract when the throttles reach the MIL detent.
I came across the non-retracting speedbrake issue on my first bolter trap, and I also replicated it on land in the Caucasus and NTTR maps, which rules out the Super Carrier module.
It seems like it is a throttle curve issue, not a Tomcat module issue. Earlier this year, I upgraded to a Warthog throttle and I've been using it with the afterburner detent installed and a curvature value of 13. If I moved the throttles to the detent, the speedbrakes would remain extended, but if I slammed them forward, it would sometimes cause the speedbrakes to retract. I increased the curvature value to 14 and now they retract every single time, and without engaging the afterburner.