They're called bridges because they connect the Matrix server to the other servers. They aren't independent. And reverse engineering protocol changes wouldn't be easier if they were.
What is discussed here is nothing new. I ran a jabber ICQ transport for myself and colleagues as far back as in 2005. It was a constant source of pain. Whenever the ICQ protocol changed, you had to wait till developers of transport updated the lib, so you could resume the service. If anything, now it is far easier for service maintainers to update the protocol because the app distribution model got much more efficient - just one tap on the smartphone, so you can just suspend the functionality until the users updates, whereas ICQ devs had to rely on users manually downloading and installing the update to their official apps, slowing the update cycle by many months/years.
