[Jiaz]

There is no enabled speed limit by default. What do you mean by *different versions* ?

You can place your ffmpeg binaries in different folder and modify Settings-Advanced Settings-search for ffmpeg/ffprobe and set full path to different binary. eg c:\\ffmpeg\\ffmpeg.exe (the double \ is intended!)
In case there will be another update for ffmpeg binary, only the one in tools/ folder within JDownloader will be updated. Customized ones won't