Things you can do:
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Execute the G28/G38 before you run your job. The job would expect the origin relative to the stock to be set before you run the g-code. While I don’t have your issue (only a Primo), this is how I do my setup. There are things that can be done this way that are difficult to do if the G28/G38 is inserted in the g-code.
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Untested, but it appears that in Repetier-Host you can define multiple printers. You could then define a printer for each machine, and move your G28/G38 to the “Start Script” for each machine. This might also work for other g-code senders.
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Enable G38 probing for your Primo and use G38 for both. I recently enable G38 for my Primo, and outline the setting changes in this topic. Note that for the specific settings I outline, you would need to give up using G28 for the MPCNC.
I did not test it, but it might be possible to have two versions of EstlCAM installed. You could have one targeted to each machine.