The old repos "belong" to the matrix foundation, but the work on them was mostly done by the element team. This is them officializing that synapse and dendrite are element branded projects, not matrix (so yes, it is indeed a handoff), except they are branding this as a fork because the license is changing.
They also are changing licences to require downstream forkers to also open-source their changes, ensuring corporate users of matrix contribute back upstream if they modify their implementation (beeper might be in some hot water, though they can very well continue using and maintaining their own fork from the matrix foundation repos with the old licence).
It requires all users, whether corporate or not, to release all changes under AGPLv3... the whole point of the Matrix protocol is to talk to other users... so basically everyone triggers the AGPLv3s "network" clause. However, releaseing your code under the AGPLv3 is not the same as upstreaming it. In order to do that, you additionaly have to sign a CLA granting the Element corporation broad and expansive rights to do whatever they please with your code... but you don't get the same rights to their code.
I agree with your assessment of the AGPL-CLA combination. But the initial part seems to be about the Matrix protocol. The projects that were forked and re-licensed are the servers - Synapse, Dendrite, Sygnal, Sydent and MAS. The protocol itself is still under Apache 2.0 (https://spec.matrix.org/latest/), though they seem to have added CLA to it. If so, the protocol doesn't have the problem you pointed out. You could use another server - like Conduit.
Beeper’s Synapse fork is already open source. Element has not had any license changes as far as I know and their applications are hard forks, meaning that even if the license changes in the future, they are safe from it.
Not sure if AGPL’s “network use is distribution” is a concern but most of their bridges are open source as well.
Disclaimer: Currently working part time for Beeper. I specifically asked the founder about this after reading the article.
> ensuring corporate users of matrix contribute back upstream
My understanding is that they are doing the opposite: by making contributors sign a CLA, they are free to sell corporate users their own private licenses, so those corporations can each keep a proprietary fork of Element's AGPL source.
They also are changing licences to require downstream forkers to also open-source their changes, ensuring corporate users of matrix contribute back upstream if they modify their implementation (beeper might be in some hot water, though they can very well continue using and maintaining their own fork from the matrix foundation repos with the old licence).