I didn't change anything in the EFI, as far as I know. Only thing that would have changed would be anything that the Mojave installer would have done.
I've done a complete re-install of Mojave on its disk, plugged in all on its own. I also did a complete reinstall of Windows 10 on its own disk, plugged in all on its own as well. And I still have the same issue. So I'm pretty sure that it doesn't have anything to do with the Mojave upgrade, since a Mojave clean install does the same.
Here's some more interesting bits. When I check the EFI partition on my Mac disk, it appears to be empty. Here's is what I did to check it.
[censored]$ diskutil list
/dev/disk0 (external, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *512.1 GB disk0
1: EFI EFI 209.7 MB disk0s1
2: Apple_APFS Container disk1 511.9 GB disk0s2
/dev/disk1 (synthesized):
#: TYPE NAME SIZE IDENTIFIER
0: APFS Container Scheme - +511.9 GB disk1
Physical Store disk0s2
1: APFS Volume Macintosh SSD 94.8 GB disk1s1
2: APFS Volume Preboot 26.5 MB disk1s2
3: APFS Volume Recovery 506.8 MB disk1s3
4: APFS Volume VM 20.5 KB disk1s4
[censored]$ sudo mkdir /Volumes/EFI
[censored]$ sudo mount -t msdos /dev/disk0s1 /Volumes/EFI
[censored]$ sudo ls -lsa /Volumes/EFI/
total 4
1 drwxrwxrwx@ 1 _unknown _unknown 512 Aug 1 01:25 .
0 drwxr-xr-x+ 9 root wheel 288 Aug 1 01:24 ..
1 drwxrwxrwx 1 _unknown _unknown 512 Aug 1 01:25 .Spotlight-V100
1 drwxrwxrwx 1 _unknown _unknown 512 Aug 1 01:25 .Trashes
1 drwxrwxrwx 1 _unknown _unknown 512 Aug 1 01:25 .fseventsd
So... I'm now lost. How does this boot if the EFI partition is blank? Does it read from the APFS somehow? Oh, an important tidbit at this point: this is an actual Mac Pro, so I'm not running Clover.