Especially your ongoing notion of metadata as private information which should be hidden is funny: how do you intend to do that? Short of wrapping your application into Tor (which seriously impacts performance letting your average family member happily pass it), I can't think of any method not including any BS-Bingo (how about a blockchain...).
I agree that the vector.im-identity service seems really unnecessary and it reminds of Mozillas approach to sync (yeaah, the ones with your cited manifesto cough); still, I was well aware that this means regularly contacting this server and probably also checking my contacts DB against it (as well as having metadata on my browser, like every other website + it's 23 ad-networks, uuh)? Also for anyone interested in actually hosting a server it's really spelled out plainly, that this is a measure for convenience and you can still host your own server – btw: did you ever try to integrate federation into syndent (you might show the world your archived Issue/PR...).
The part about the integration server is indeed worrying (but not you, putting at the end?!?) because without it, I don't really see the value proposition of matrix compared to plain old XMPP (and I wonder how you intend to monetize on kamax...). And I wasn't really aware of it...
The other parts
- I didn't give an eMail, wasn't a problem for me and I'm seriously not imaging any way to resolve this w/o aforementioned BS-bingo or yet another personal information (private/public key, which is beyond scope for most people + creates its own set of problems (people with unencrypted keys on their machines...)
- so the only way for matrix to read messages is by adding a bot? can the scalar.vector.im server initiate that too? otherwise your claim that vector.im can read all your messages is just BS
- you never mention that encryption by default would be cool. How will kamax.io handle this?