Interesting! How does Matrix relate to red#matrix [1] and the Zot protocol? Not asking because both projects contain the word "matrix". Both projects seem to overlap. Would like to know more about how they differ and how they relate.
There is no link between RedMatrix and Matrix.org - the fact that both have Matrix in the name is total coincidence. On the Matrix.org side, we came across RedMatrix for the first time a few months ago when stumbling across http://lists.w3.org/Archives/Public/public-fedsocweb/2013May... in Google, which then linked from Friendica/Red to RedMatrix.
I've never played with Friendica/Red/RedMatrix/Zot, but from what I can see, it's more about federated blogging/social networking than messaging or pure JSON synchronisation like Matrix. Architecturally I'm not sure how they compare - I only just found https://github.com/friendica/red/wiki/zot; we'll have a read and see what the difference is.
Something we're very keen to do with Matrix.org is to build as many gateways and bridges through to other comms ecosystems as possible - so the fact that both Matrix.org & RedMatrix (& Diaspora & Identi.ca & all the others) are operating in a similar space isn't at all a problem - so long as they all talk to each other. It'd be a bit embarrassing if we were building federated communication systems which couldn't gateway to each other!
[1] http://redmatrix.me/