I've tested this, and I admit defeat.
Here is what I've managed.
When I have a computer with something already installed on the hard drive
I install Ubuntu onto the USB. Thereafter, the only way that I can boot into the USB drive is to remove the hard drive (!), and even then it takes some fuss to get the USB to boot. After booting, it goes to the Ubuntu logo, and nothing more happens. However, if the hard drive is in the machine, it boots normally to the hard drive.
When I have a blank computer to start with
I install Ubuntu onto the USB. This works normally.
Then, I install something else onto the hard drive, ignoring the USB.
Thereafter, if the USB is in the machine, it installs normally onto the USB, and if the USB isn't in the machine, it installs normally onto the hard drive.
So, it seems that it works if you install onto the USB drive first, and then onto the hard drive.
You might have different results, of course, depending on hardware and the specifics of your installation.
Unfortunately, at this point, my lack of technical knowledge lets me down and I cannot take this any further. I don't understand why this happens, sorry.
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