Honestly I think Mastodon should remove the DM feature from the UI given the nature of the AP protocol. Even if you encrypt the message contents it is still always going to be public information that you sent something and who you sent it to, given how ActivityPub works so given the reasonable expectation of privacy that comes with a feature like DMs, which AP just can't do, remove the feature from the interface so people know to use something else for private communication.
I guess this is also always going to be a weird side-effect of interoperability. Even if some clients/servers disable it others will still support it and sell it as a feature without properly communicating the problems.
Honestly I think Mastodon should remove the DM feature from the UI given the nature of the AP protocol. Even if you encrypt the message contents it is still always going to be public information that you sent something and who you sent it to, given how ActivityPub works so given the reasonable expectation of privacy that comes with a feature like DMs, which AP just can't do, remove the feature from the interface so people know to use something else for private communication.