From my understanding of how this works that's mostly a consequence of the Tor browser trying to achieve network privacy and anonymity at the wrong layer.
The right way would be to route all the requests through Tor, not just those from the engine of the browser.
I used to be of this opinion, but [1] changed my mind.
The problem is that there's a huge potential to deanonymize the user at an exit node because of all sorts of traffic other than web browsing. Do all of your chat programs encrypt everything? How about your email client? What about every daemon on your system that accesses the Internet?
At the very least, all of these can be used to fingerprint you.
WebRTC is a great example of why the user-agent turns out to be the right level to think about anonymity over Tor.
The right way would be to route all the requests through Tor, not just those from the engine of the browser.