Hi Jared,
You request makes complete sense. We will have this in mind for the future. The workaround you can follow is, first, follow Soil and plant masking w/ Pix4Dfields.
Soil masked map
Formula:
(nir-red)/(nir+red) + 0/max(0; (nir-red)/(nir+red) - 0.4)
Once you mask out the soil, you can run the Magic Tool over and select all the area of the new orthomosaic.
Let us know,
José