Whenever cover products are generated in MAPEO (both for RGB and MS flights), mask (or mask-ms) products are also generated. These products are a binary mask of crop/no-crop, and allow you to extract statistics per layer based on the crop cover alone.
If you have mask or mask-ms products that you would like to use for extracting masked plot statistics, you can follow the steps described in How to export plot statistics?
After selecting whether you would like to export your statistics in CSV or shapefile format, you will have the option to Apply a Mask:
You can either apply a Mask, or a Mask-ms, which will be determined by whether you are extracting plot statistics for an RGB or MS flight, respectively. Selecting a mask and continuing with exporting plot statistics will result in masked statistics that only take into account the plant cover, and not the surrounding soil in the plot. If no mask is selected, plot statistics will be exported as previously, including the soil in the statistic calculation.