Interesting results. I think it's important to note that RF, AV and s-video will all give potentially different results as to output quality. RF output on the 2600 is in fact cleaner with the Traco's, but that's all I tried. I think it would be interesting to put high and low pass caps on the Traco output and see what your results on the Genesis are.
I have also been experimenting with switching power supplies on the 2600, with good results while using Traco's. Horrible (predictably, I know) without.
There is a tremendous amount of room for improvement on the 2600's as far as filtering, as their filtering is absolutely terrible :-), yet still they work, and have worked for many tears. Atari was so cheap in this area - they did the absolute minimum. Still, for a few pennies in parts, it's AMAZING what you can do.
I've got a 2600 that I've been experimenting with, if there's interest I can post results and video. Of note - I've done nothing to it that couldn't be undone... but I've modded it to pieces. I think you could put a blender on top of it and it wouldn't affect the RF :-)