So does this pretty much boil down to "we are re-licensing Synapse and Dendrite from Apache to AGPL"?

In what way is the "owner" of the code significant, in this case, other than being a proxy for the maintainer of the most popular fork?

These projects are open source, so the only thing this code is really attached to is the license. Whatever entity controls the majority of developer effort effectively controls the future of the project. So far, that entity has been Element, and the features being worked on in the client and server applications have been and will be influenced by the customers of Element and the sponsors of the Foundation (for an example of this influence, see the biometric/PIN lock introduced in the Element X mobile applications).