When making physical keyboard shortcuts you can easily differentiate between the left and right modifier by enabling BTTLeftRightModifierDifferentiation in the configuration. However, it is not currently possible to make a touchbar button trigger that differentiates between modifiers.
Manually editing the command key (55) to the right command key (54) changes the text in BTT but it does unfortunately not trigger the right key.
I would love to see this feature added.