The "Preboot" volume only gets put in the container after an install, and after you convert to APFS it shouldn't affect booting. I installed Mojave onto a HFS+ disk, then converted to APFS and booted back in without issues, as I have done may times. Right now the only disks in my APFS container is my main boot partition and the VM disk, and nothing is affected. When converting to APFS, I assume it creates an invisible Preboot partition which isn't visible until you run a reinstall on the disk or an update. I have done a lot of testing on this.
With the APFS patcher, you will not be able to have a bootable recovery partition. That's just the nature of working with things on unsupported devices. This shouldn't be an issue, since a bootable installer has all the same elements as a recovery partition. Your USB stick with High Sierra should be more than enough if you ever need to use a "recovery" feature.
The EFI Boot option is just an error in the code of the APFS Patcher according to
@dosdude1, as said
here. This is an arbitrary option and does not affect booting into APFS. Just select your main boot partition and everything will be smooth sailing, for the most part. Hope this helps!