To export an Quicktime AMA sequence (such as Canon DSLR clips), you can export an AAF without creating Quicktime Reference files.
To do this, you must enable “AAF Edit Protocol” and Export Method should be “Link to (Don’t export) Media”. In After Effects Auto duck import dialog, select “Connect After Effects directly to Avid media files”. AE will then link to your source files.
This only works with AMA files that AE can read. When dealing, for example, with MXF sources, you must select “Create QuickTime reference movies”.