Improve handling of FLATPAK_BUILTIN_FLAG_ONE_DIR

Error out for all combinations of options that specify
more than one installations.

This was showing up e.g. with

flatpak config --installation=extra --system --get languages

Closes: #2511
Approved by: mwleeds
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Internal Server Error - Gitea: Git with a cup of tea
500 Internal Server Error

Gitea Version: 1.28.0+dev-477-g8b6ad49a5f