I have the feeling you know all of that very well, however – as I write in a forum, I have to be a little bit more sharing and detailed. Having said that:
With the “.aec” file, one doesn’t even have to deal with all the single sequences. It just loads them in with a click or two.
Yes, I wish Adobe would use OpenEXR multilayer files like NUKE does.
Not to argue here, but many parts of the Multi-Pass system need floating point. I found it always rather weird to clean up QUICK Time Multi-Pass files for Ae use, e.g. when “alpha channels” (Buffers, data results, etc.) are delivered in the RGB channels and set up as gamma-based for example.
Again, since I have no experience with Win7 and what QT is available for it, please check with the support.
Fingers crossed that you get your wanted set up working.
My best wishes