I am both a Reaper and Ableton user, though more Ableton these days. I am in a similar situation where I want the FCB1010 board buttons to change which preset sound I have for the one track, much like for the ancient midi where you used program change requests. The solution I found may be of use to you "The Pirate Kings", first up the good news there is a simple solution to your problem, the bad news I could only find a solution in Ableton not in Reaper. The solution is simple enough so you only need Ableton Lite not Ableton Max. Ableton Lite is what I use.
For this example my instrument is an audio instrument (electric violin). One of the effects I have in Ableton is the "Bandpass Spiner" which I use a filter and drive. I have various presets for this effect and wanted to use the foot pedal buttons to switch from one preset to another. On the Ableton side drop down the "Audio Effect Rack" and enable the chain list, drop a copy of each instance of the "Bandpass Spiner" each with your own preferred configuration, to the right of each chain is the mix level, set these to unique numbers, say 1 for preset 1, 2 for preset 2 and so forth. The mix level is then attached to one of the "Audio Effect Rack" knobs, which in turn you link to say midi controller ID 50, so as you change CC 50 it selects your different presets. On the FCB1010 side, program so say button 1 sends a CC 50 value 1, button 2 sends a CC 50 value 2 and so forth; also if the expression pedals are to do some thing as well program them appropriately.
Clear as mud? Here is a screen shot of it in Ableton:
Zooming in a on the effect preset, I push foot controller button 1:
now I have a Wah wah, where the corner frequency is controlled by expression pedal A.
I now push foot button 4:
I now have turned off wah wah with a flat EQ curve but have turned the drive up to full bore at 24 dB.
A similar approach could be taken with midi feed VST's.
I could not find a similar feature in Reaper, was hoping I could set multiple effects on the one track and use a channel router to say which effect gets to be active, ie pin connections but could not get this to operate as desired. The channel router would be connected to one of the CC's on the foot controller. Maybe someone else has a fix for this using the pin routing matrix.
Agree, using a different track for each effect is not good. Switching tracks mid way of a recording is a nightmare.