I experienced this too and the way I fixed it was to keep going back and forth between the black and white paint map, inverting the surface and painting to make sure I’m capturing the surface. By default the "Strength’ on the paint tool is set to 0.5. Try bumping to 1.0 and paint over the areas where you are getting spikes.
You may actually see very small values on the ‘InnerFat’ vertices in the spreadsheet, and I think this may be contributing to the spikes. So paint/repaint as I mentioned above to clean up those values.
It can be a bit tedious, and we realize the painting tool in general needs a bit of love and will address that in the future.
