I'm using 1.3.1 with SSTU and RO.

The masses of engine clusters scale by 2n-1 instead of by n. This is caused by the "origMass" field in the RO engine configs. Simply deleting that line and assigning the engine a value with @mass outside of the module as in stock fixes the bug, however, then different engine configs cannot use different masses.

Something about SSTU appears to be taking that value and adding it to the mass when engines are clustered.

SSTU does not touch, read, write, or use any fields from ModuleEngineConfigs. This error exists entirely on the side of RealFuels.
Edit: More specifically, all that SSTU does is pass in the number of engines in the cluster as a 'scale' value to ModuleEngineConfigs. What happens past that point is entirely outside of my control.

Please bring your issue up on the RealFuels repository, as this is not a problem that I can solve.

You already did solve it by providing the adjustMass KSPField in SSTUModularEngineCluster, and i'm very happy about that. :)
RO hasn't used it but i opened a PR there to set adjustMass to false which causes mass calculations in RO to be correct.

Thanks for the confirmation and info. Thought that this had already been solved at some level...