Sorry, but Natron is reliably routing the quality controls to FFmpeg for rendering.
Try to pass the same options to ffmpeg, you should get the same results.
For the documentation on each codec, you should take a look at the ffmpeg documentation.
The bitrate, as in ffmpeg, is in bits per second.
One problem is that, as documented in Natron, these settings are "Only supported by certain codecs".
bitrate is supported in avc1, hev1, MP42, 3IVD, but not mp4v.
bitrate tolerance is supported in MP42, 3IVD, but not av1c, hev1, m2v1 or mp4v.
quality is supported in VP80, VP90, avc1, but not hev1 or mp4v.
Keep in mind that 400000bps is very low for HD high quality video. 5 000 000 is a better target.
The general recommendation is to use use either separate frames, or an uncompressed video format, or a "digital intermediate" format (prores, dnxhd), and to transcode the output with a separate tool (such as the ffmpeg or mencoder command-line tools, and there are several GUI tools around). ProRes works very well on windows if you use the right tools (VLC, ffmpeg, mplayer, mencoder).
Believe me, it is very difficult to have a generic interface for different codecs, because each codec has its own parameters.
We will work on having easier settings to avoid transcoding when we add audio support. For now, you have to mux the audio anyway, so please stick to the recommendations.
I updated the doc in WriteFFmpeg accordingly