is there a way to disable a drive bay from the command line?
Create a small JHFS+ formatted partition. Install the rEFInd Boot Manager to this partition. Configure rEFInd to silently boot Mojave. If configured properly, rEFInd will appear in the Startup Disk pane of System Preferences of Mountain Lion. You then can select rEFInd from Mountain Lion. When rEFInd boots, the software will silently instruct the firmware to boot Mojave.
A simpler alternative may be to rename the System/Library/CoreServices/boot.efi  file in the Mountain Lion startup volume. The may prevent Mountain Lion from booting, which may result in Mojave booting.