Can I get Sierra to boot from USB EFI partition?

I always boot from USB, auto-selecting my HDD installation by adjusting the Clover config.plist file accordingly. I notice that with the latest Clover version (maybe in prior versions too, but did not notice), the boot file is always written to the root of the USB. I would like to install boot in the EFI partition, where I have installed the Clover files, and have it boot from boot in the EFI so I can delete boot in root without breaking the USB.

Can it be done?...

Can I get Sierra to boot from USB EFI partition?