Don't upgrade firmware from USB installer, do it from macOS. Read here to know what you have to do: MP5,1: What you have to do to upgrade to Mojave (BootROM upgrade instructions)
Didn't know this. I've been upgrading my Boot ROM from a USB installer. I'm using a USB 3 card with a USB hub plugged in. Done it 3 or 4 times now without issue
Lou