For the F-Droid build Conversations and some of its fork switched to using the newer builds eg. 'ch.threema:webrtc-android:100.0.0' provided by Threema for their own Android app.

The issue is that their build is patched for their needs: https://github.com/threema-ch/webrtc-build-docker/tree/master/patches

And some Conversations forks (Cheogram, Snikket and Conversations from Play Store) can't use that since the patches break calls with https://jmp.chat users.

Is Stork affected by those patches? Can the Threema build be used?

The current lib provided by Google in maven, that Stork uses, is already >2years old and many CVEs have been fixed, eg. https://gitlab.com/fdroid/fdroiddata/-/merge_requests/11496#note_1047414675