LAUNCHXL-CC1352P: Change Board in CCS conflicts with SysConfig

It may be easier to import an example from the SDK based on the LAUNCHXL-CC1352P-2 to get the correct setup in syscfg and then import your application files into this project. 

I understand that would be a workaround, but is there no global setting for the board selection I can change that I am missing?

You can also try 

(Select Board View, upper right corner in the syscfg window)

To be on the safe side, take a copy of the project before you try in case something goes wrong in the swith.