I disagree, the use of MongoDB reflects poorly on the future of the project. In my opinion, a custom protocol does not. They intend for the app to be an alternative to a giant like Discord, so the protocol being custom leaves them with the freedom to introduce features Matrix didn't consider.

In opposition of NIH syndrome, using others work often locks you into the framework of their thinking, which can often be flawed. So to make improvements within the framework, you must think outside of it. Matrix might not be flawed, but it is purpose built for a specific task, a task that likely won't capture all possible use cases of this project. Perhaps it would be the right move to use in the beginning, but once the project matures it may become a limitation.