@Shoggoth43 It's been a while but I seem to have resolved the problem.
First I releveled the bed and have gotten it to within .2mm across the plate so that has improved. This really didn't do anything to resolve the main problem but it is at least an improvement. I may work on that a bit more as it should be easy enough to improve, but this was done mainly to see if I could find a workaround in case I couldn't get the mesh compensation working.
Due to having to manually add/remove the probe I would manually create a bedmesh and save it. Given how warped the bed was and the bed compensation issue, it was taking way too long to try and do a full mesh with each print. Whenever I rebooted the printer I would reload the mesh with a macro that did a G29 S1 and a M376 H5 to set a height taper. I would confirm the bedmesh compensation was in use with M122.
I had glued small bits of filament on top of the Z screws to confirm that any X or Y movement using the PanelDue or other gcode commands did, in fact, use the compensation when the bedmesh was enabled using the macro. However, it would not compensate most of the time when running a job. Sometimes it would work, but most of the time the nozzle would just end up too far from the bed in places and fail, or I would have to babystep it so close it would tend to auger into the bed surface or the extruder would just skip/clog/jam instead. The bed is currently now flat enough that a .2 mm 1st layer height probably won't gouge into the bed but I will need to work on that a bit more.
The apparent fix may be one of those dumb "everyone knows this" bits but adding the G29 S1 command to the actual slicer start gcode seems to have resolved the issue. I still haven't found anything in the documentation to indicate that this should be required given that the M122 command shows that bedmesh compensation is in use, but it seems to have fixed the issue for the moment. I tried several slicers while troubleshooting but it may not be in the start code of all of them so that could have been part of the problem in tracking this down.
I still need to reset my Z offset after a nozzle change and I seem to have some under extrusion issues, but the bed compensation issue now appears to working reliably.