The short answer to "can Calibre do it?" is "yes." The long answer is, "yes, but it's complicated."
Take a look at the CalibrePEX GUI under PEX Options > Netlist > Format. Right under the "Ground node name" option you named is "Ground layer name". This is what you're looking for. However, using it is tricky, because, usually, the right answer is a derived layer name that is buried in the Calibre rule deck. Most of the time, an SVRF PEX deck puts all of your N-well, isolated P-well, etc. layers through some logic permutations to come up with layers that are fit to use in DEVICE statements for the backgate tap. Those layers are the ones you want to put in the "Ground layer name" text box. The formatter will tap parasitic caps associated with those layers to whatever nodes the layers connect to. That gets parasitics associated with your PFET N-wells to tap VDD instead of VSS. It should work just as well for isolated P-wells.
Wish I could be of more help, but it really depends on your process and your rule deck. It's possible there are marker layers in your process specifically for the purpose of indicating analog grounds and wells, but you'll need to look at your process docs and/or the rule deck.
For more info, check the PEX Ground Layer docs in the SVRF manual and maybe hit up SupportNet.
Vern