Avid works by rendering down layers. This is fine in a HD fully uncompressed format. In everything else it degrades the image quality. Avid’s system allows layers to be compressed and then recompressed multiple times. I hope FCP never adopts this solution, but remains, as most compositing applications do, with rendering only from the source media.
There seems to be issues going back and forth with QT material. Could you give full specification of the audio, what is it, and what the track structure is?
What’s that mean, I have to separate the bins manually? What’s the layout and what happens when you create it, apply it? FCP always had problems with some layouts, overlapping windows, cross monitor windows. I haven’t seen one that’s bin specific.