What is the best way to get list of retired packages in F35? I can get list
of all retired packages by scanning dist-git. But if I want it for one
release of Fedora? And I do not want to do that manually; I rather want to
script it.

PDC would be your source of truth for this info. You'll need to look at the
"active" state of the package/branch.

I got to weird package

  flatpak-runtime-config

This:

  https://src.fedoraproject.org/rpms/flatpak-runtime-config

indicate that the package is retired (because it is only module package). And indeed:

  https://koji.fedoraproject.org/koji/packageinfo?packageID=24302

It seems to be built in MBS. But repoquery cannot find it:

 repoquery --releasever 34 --repo={fedora,fedora-modular,updates,updates-modular}-source flatpak-runtime-config

And PDC is either misbehaving or I cannot use it properly:

https://pdc.fedoraproject.org/rest_api/v1/component-branches/?name=flatpak-runtime-config&type=rpms#tab_list

What is current status of this package? And how can I verify it?

Miroslav