wow:
We use specifically crafted messages that trigger delivery receipts allowing any user to be pinged without their knowledge or consent
That makes think that 1st, perhaps it would be a good idea to avoid "return receipts" on any messenger, though that breaks ability to know if the destination has actually received, and if the destination has actually read the message.
Perhaps another thing, even though your messenger doesn't identify users with phone numbers at all, still block the messenger to have access to your contact list. Not sure if this affects, for example if a xmpp client has access to a broader contact list, if it can only relate to xmpp addresses it wouldn't pay attention to phone numbers, but I can't really tell.
And of course, don't use any messenger which tights users with phone numbers, no matter if to share among contacts now usernames are used instead of the phone number, when the phone number is still the way to identify the user.