why all they did was separate the FileVault drivers from the standard install its still the same just less clutter. the old installer installed a bunch of un necessary drivers that are only needed for file vault.
depending on how old your smbios is on your config.plist you might have to update the bios info. if yours is too old mojave might be trying to flash the real mac smc bios onto your machine.
are both bios at the same revision? look for differences between them. if you want to see if it is hardware or os related swap your drives and see if the issue transfers. these are all basic troubleshooting tips for any system.
in linux make sure the partition has not changed partition type correct it if necessary . you can check in linux disk utility. g-parted might have issues with it.