An update on this issue. (BTW could a moderator please change the title to "RPI 5 USB boot issue" as it might get more exposure?)
I posted the same question on the Raspberry Pi forum and was led to there being a potential problem with libreelec.
I'm unsure if external links to other forums are allowed so in summary I listed my le cmdline.txt and output from blkid -o list to show that the UUIDs were the same (this was with the working le12 system running on a usb2 port) and confirmed that another os (bookworm installed on an ssd connected to the usb3 port along with the hdd on the other usb3 port) did boot as normal.
The response was:
quote
That looks like libreelec is doing something funky with an initrd. It's probably best to ask them for help. It'd been years since I last used it.
unquote
Just to clarify - there is no issue booting le12 from a usb stick attached to a usb3 port as long as there is no hdd attached to the other usb3 port.