Reaper's routing lets you do almost any damn thing you want. There are all kinda of ways to get to your hardware outputs that have absolutely nothing to do with the Master track itself. By default, though, everything that's on the left channel of a top-level track gets summed to the left channel of the Master and likewise all the right sides. It has no way of knowing (and doesnt care) whether that's what you recorded or the FX you put on it. When you click the Master mono, those two channels get mixed together, attenuated 6db, and output to both channels which then get routed to whatever hardware device you've assigned.
I have a couple different setups where the Master doesn't actually do anything but meter - it has no hardware outputs of its own. In those setups, the mono button won't change what I hear, but does still affect the metering.