Apologies for the thread bump, but I'm confused about exactly why this is a problem, and there are several scenarios going on here, which as far as I can tell are:
1) Install Clover onto a real Mac's EFI partition on the boot drive
2) Install Clover onto a USB, boot it and run the installer on a real Mac's boot drive, going through to the rebooting stage
3) Install Clover onto a USB, boot it but don't run the installer; for example, restore a Time Machine backup or run Disk Utility.
I can imagine 1) won't do much good; you're overwriting the right EFI kexts with totally wrong ones, same for 2). But I can't imagine 3) being an issue, as at no point would you expect any data to be written onto your boot drive. Indeed, that sequence would work regardless of what other disks you had in the drive. How exactly could this trash the boot ROM?