Originally the FW update via QGC worked, and ideally that would be the way it works, but at some point the update stopped working (note that our bootloader didn't change).
The px_uploader tool to me uses the same protocol as QGC, and as this works, I have a hunch the issue will be QGC side, but the jury is still out while we track it down.
I decided to proceed to ship Flight Core v2 as I found the work around acceptable and had the work around publicly documented. I agree that our product line is still a bit bent towards power users at this point, so the use of git and such is a big ask for most people.
If you have the chance, with respect to this topic in particular on this thread, please let me know where you got stuck with this particular process with our documentation and then I can use that feedback to improve things.
https://docs.modalai.com/flight-core-v2-firmware/#how-to-upgrade-using-px_uploader-tool