Thunderbird is a messaging/communications client, and way more people will benefit from Matrix support than would ever benefit from Maildir support.
Further, my understanding from the Thunderbird team's comms is that they are very much in control of their own destiny. I don't get the sense that Mozilla has much say in Thunderbird's roadmap (or even cares) at this point.
It's an email client.
Absolutely yes. Maildir support is a niche want, where as chat has become essential for many offices replacing email for most internal communication.
Additionally the chat fuctionality has been available in one form or another for years but has been quite neglected. They have just finally extended it and cleaned it up
You can keep logs from a Matrix server if you configure it to do so.