create-usb: Don't look for runtimes of runtimes

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Currently the create-usb command looks for a runtime for every ref
passed to it, whether it's an app or runtime. This leads to an error
when a runtime was specified because runtimes don't have runtimes.
Normally you shouldn't need to pass a runtime to create-usb because it
finds dependencies on its own, but you conceivably could (and in fact
the eos-updater-prepare-volume tool in Endless does in order to make
sure an icon theme "runtime" is included with OS updates).

This commit fixes the issue by only checking for runtimes for apps. The
way it's written takes extra care to ensure the FlatpakKinds value used
is based on the ref value used, to protect against the case where one ID
exists in multiple installations with a different kind in each one, even
though it's hard to imagine that happening in actual use.

It's difficult to add a unit test for this at the moment since the unit
test for create-usb is blocked in
https://github.com/flatpak/flatpak/pull/1877

Closes: #1924
Approved by: treitter

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