I understand the issue you are facing, in order to exclude the soil from the index map generated there are two options currently. The first would be to use a custom index where the formula is adjusted to try remove soil from the values returned. However, if you are using NDVI and working on the index values associated to this I would suggest the second option.
Pix4Dfields is our product dedicated to agriculture (, we offer the ability to import your drone images, create an orthomosaic and from this generate pre-made indices or custom index calculation. If you wish to use the NDVI index this can have the values clamped to remove the extremes (e.g. the soil). To do this click Index Generator, then Create a Custom Index and input the following formula:
(nir-red)/(nir+red) + 0/max(0;(nir-red)/(nir+red)-0.2)
Note: change the 0.2 value to change the constraints (e.g. 0.2 value here will remove all values below 0.2 on the NDVI scale, 0.4 would remove all values below 0.4). For more information about the index tool see here: https://support.pix4d.com/hc/en-us/articles/360000891623
You mention the use of prescription maps, we offer the ability to create zonation and prescription maps within Pix4Dfields, however the zonation would struggle with the custom index mentioned above because we have removed low index values and created a hole in our map.
We are working on tools where areas such as the vines will be detected and automatically only calculate the index on the areas of plants and exclude the ground, this tool will come in the near future.