I know that this is probably a very specific use case, but I have a program that generates some FFmpeg video filters based on the contents of a replay, to put live data on screen. However, this makes the command often very long, exceeding the 500 character limit. It would be very helpful for me if this limit was removed, or at least raised by a lot.

Since you obviously are an advanced user, have a look into render queues: They not only contain the camera path, but all render settings, including the FFmpeg arguments. So you could add an entry to your render queue and edit the arguments there.
For that, open up the MCPR file with a zip-program and get the renderQueue.json file.