What is the purpose of XDG_CONFIG_HOME in Flatpak applications config directory?

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I started developing an application to backup Flatpak applications.
According to Flatpak documentation, application configs are default located in ~/.var/app/<app-id>/config.

What I don't understand though is that the base directories of this path is XDG_CONFIG_HOME which defaults to $HOME/.config.

If I understood correctly, the path for application config is constructed like this : $XDG_CONFIG_HOME/~/.var/app/<app-id>/config. But then this is the same as only ~/.var/app/<app-id>/config.

So, what are the differences between using $XDG_CONFIG_HOME/~/.var/app/<app-id>/config or ~/.var/app/<app-id>/config ?
And what I misunderstand ?

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