docs: Clarify flatpak override merge order and scope

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The override man page mentioned global vs per-application files but did
not say how the system and user layers combine, whether system-wide
overrides affect apps from a per-user installation, or how conflicting
settings such as share/unshare resolve.

Describe the storage layout and the command-line selection of the
target file separately, document the merge order implemented by the
deployment code, and note that system-wide overrides only apply to
applications in a system-wide installation.

Closes: #6478

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