I am trying to install Qubes OS Linux on my Mac mini. However I want to install it in a MBR configuration on a separate internal HDD.
Is there a way to configure a mac to boot a MBR disk instead of UEFI?
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I think you mean "GPT" instead of UEFI. UEFI is a type of firmware interface capable of running a bootloader, GPT/MBR are disk partition table types.
Now to actually answer your question: Yes, you sure can. However, editing UEFI boot entries is a bit fiddly on a Mac, as I don't believe it follows UEFI standards. As such, I would recommend using rEFInd to generate the boot entries for you.