In other words, what you did is perfectly fine, but if it is a pain to do manual edits on a regular basis, then either modifying the LVS setup file to suit your needs or modifying the xschem diode symbol is a more permanent solution (assuming a square diode, the schematic can generate the perimeter value from an expression 4*sqrt(area)). You can also just waive property errors if you have looked through them and understand that they are all false positive errors. Note that you are getting values like

area=400

for the diode area extracted from layout, which is going to cause property errors regardless of what you do about

pj

. This value (which comes from incorrect assumptions about how the SkyWater 1e-6 scalefactor gets applied in the case of model level 3 diodes) is from an earlier version of the PDK and has since been corrected (after a long discussion with Stefan Schippers about how those values operate in ngspice simulation). You probably want to update the PDK so that the extracted layout produces correct area and perimeter values (which are in bizarre units, as you can see from the schematic values, which are actually correct).