i mean you can always go mono or duo language and then it is really not that of an issue
Assuming you were using Protobufs as they are usually used, meaning under generated code, I saw no difference between using it in Javascript and any other language in my experience. The wire format is beyond your concern. At least it is no more of your concern than it is in any other environment.
There are a number of different generator implementations for Javascript/Typescript. Some of them have some peculiar design choices. Is that where you found issue? I would certainly agree with that, but others aren't so bad. That doesn't really have anything to do with the browser, though. You'd have the same problem using protobufs under Node.js.