I sent a message to dosdude and he said that you just need to select your startup disk and everything will boot fine.Try to restart your computer into the DosDude USB, reapply the patches and don't select the apfs patch option.
If that doesn't work, reinstall the Mac OS over the disk from the DosDude USB and don't select the apfs patch option. This will not affect your files.
With all this talk of BootROMs and EFIs, I got to wondering. I installed the APFS Update successfully on my 3,1. Did get verbose start up for the first couple of startups then they went away. And now I am back to a normal boot screen.
I have been doing a lot of everything and have to reboot a lot. And in doing so I usually have boot through Startup Manager. There I see all the bootable volumes. But in with them are 3 EFI volumes that implies that they can be booted from. They are just marked "EFI".
I have never tried not knowing what they could do. But in all the pics posted I haven't seen them in other Startup Managers. I trust that there's one per OS that might need them for whatever reason.
Is there anything I should know about or can do with or to them?
if you do the boot rom patch it wil give you 2 efi drives per os. This is a glitch.
watch this video for more information: