Is this Ok or not? Cloning / Clover / Copying EFI

[powerpcg5]

For some reason, the Multibeast post install tool doesn't work on my machine. I mean, I can click Build, it seems to run and seems to be copying files, but when I look at the EFI partition, it's empty.

On my initial El Capitan install, I tried Boot EFI, Boot-Legacy, Boot-Legacy-Root and nothing worked, i.e. can't boot from hard drive (only USB stick).

So had an idea... I mounted both EFI partitions on the USB stick and Hard Drive and manually copied the files from the working USB stick to the Hard Drive and voila! Now I can boot from the hard drive!

I then created a cloned second hard drive. First, I formatted the new drive using Disk Utility, run SuperDuper! on it, then again, I coped the EFI partition from original hard drive to the the cloned hard drive. Now, the cloned hard drive can successfully boot too (yay!).... but it doesn't have the Recovery and Tonymac partition. I don't know what these partitions are for.... (anyone?)

So Question.... is this method (i.e. manually copying the EFI partition files) okay? Am I setting myself up for trouble in the future?

 

[powerpcg5]

Another follow up question:

What's the difference between the config.plist found in the EFI partition, and the config.plist found in the Hard Drive partition?

The config.plist in my hard drive have more entries (<key>Fixes) than the config.plist in the EFI partition.

Which takes effect when booting?

Do I need to copy the config.plist in the Hard Drive to the EFI partition? so they both match?