Thanks for responding Axel.
I have been using x264 encoder due to QT's notorious gamma shift as u mentioned, but u gave me the idea of using QT again. With the gamma shift, the final export actually looks very close to what i saw in my timeline. A happy accident.
I think I need to do some tests with editing the all-i right on the timeline. I've always transcoded to ProRes first because it feels so much faster on the timeline.
To answer your questions, yes, even with the EOS plugin the mkIII footage cannot be ingested via L&T.
Admittedly the mark ii has the luma troubles as well, but it doesn't shift in color.
Even if I do export a master in ProRes, I still need something to reliably convert it to H264 for web... something I don't currently have.