I'd love to know if you ever got this working.
If I was to look into this, my first pass would likely be to use gRPC for Java or Python since MATLAB can talk to either language. My experience with both bridges is that they are pretty slow. It's also possible to call C++ directly from MATLAB. I've done that much less, but it's definitely faster if performance is a concern.
Of course those sorts of integrations only work well for one time integrations. If you're looking for a general solution that can start at any .proto file and generate appropriate MATLAB class files then it sounds like you were on the right track.
