How many boards per panel? How different are the two BOMs?
I would think just sending gerbers for the whole panel, BOMs/PnP files for the individual variants, and instructions for which panel instances get which BOMs should be sufficient. It's not that different from having the CM do the panelization for you--which would be another option you have.
Unless you have a reason to want the two variants panelized together, it may not be that big a deal to have the CM do two runs with homogenous panels, depending on quantities.