I have spent extensive research hours into the exact issue that your experiencing. Yes, your mac has booted via its "last effort", or "fallback mode" and used an emulated BIOS to boot. An OS booted in this manner cannot see any EFI interaction with the hardware.
Macs boot via EFI, some models look for a FAT partition with efi binaries, and some models (like my macbook) require an HFS partition with efi binaries. The latter does not follow the standard.
The boot order is programmed into the macs EEPROM, and that is how the mac knows where to look.
Here are some steps (i will not show you how to use each utility):
- boot from rEFInd's USB image, by holding alt at boot
- use the rEFInd boot menu to boot your ubuntu installer (this ensures that the OS knows it booted via EFI)
- install efibootmgr from the official repos
- use efibootmgr to manipulate the embedded EFI boot settings in the macs EEPROM
I have had great successes using the links above.