There is a formal process for that. First, a messenger must register with Roskomnadzor (a government organization). So if a messenger is not on the list, it doesn't have to share anything yet.
What i think about it: why not build in ToR client right into the app itself, make it update itself, then always use ToR with obfs4, and openly declare that there will be no compliance, and you can't do anything?
Only concern could be the file size, but Orbot is only 12MB for example.
It will also greatly increase popularity of the messenger.