After much digging and a response from Line 6 I've found a way to do this in Reaper. Just updating this for posterity!
1) Set up a track in Reaper
2) Add the Helix Plugin
3) Open the plugin window
4) Click the + button (next to the No preset drop down and the Param button at the top of the window)
5) Click Link to MIDI program change and choose an option
6) Click the + button again and click Save preset
7) Make another preset
8) Add a MIDI item to the track, or another track and send the MIDI to the first track.
9) Use the Bank/Program Select option in the automation.
10 Set the Program number to the desired preset. Note that MIDI is 0 based, meaning the 128 options starts as 0 and goes up to 127. So preset 1 is 0, preset 2 is 1, etc.
In testing I found that there is still a delay when switching presets (unlike snapshots). Switching between the first 2 Factory patches had audio gaps between 25-75 ms. These were also delayed. So you'll want to move the Program Changes forward a little so the delay and gap happen at the very end of the section and the beginning of the new part has the proper sound.
I DID find that rendering stems, freezing, or even full project renders seem to have a bug when doing this. They don't render fully. Posted that on the Reaper forums looking for help.