Just my 2 cents worth:
By coincidence I've been forced to deal with this issue myself recently. I'm out-putting lip-synced toon-shaded animation at 24fps to be posted in After Effects and Premiere Pro CS5 (I bought CS5 in 2010 for a project and it still works great!).
Because of I-clones eccentricities, I'm forced to output audio as an mp4 at 30fps, and the picture is a PNG sequence at 24fps. The picture might comprise of three passes per character ( 1-with lines, 2-without lines, 3-matte pass) and then some motion tracking data if necessary (another pass or more) -- so I have to keep notes. I block the scene, set up the cameras and lights, use the switcher to figure out the coverage, then render each angle based on the switcher cut -- but with a few seconds either side of the cut to maximise my editing opportunities. That last part is a lifesaver. All four files (three PNG picture at 24 fps, and one MP4 sound at 30fps) are pulled into After Effects and synced up into a single composition (very fast). This is then rendered into a Quicktime JPG sequence for editing. Any additional work (adding backgrounds, etc.) is done in AE and then re-rendered as necessary. These re-renders update automatically in Premiere.
If I could make it simpler I would. However it guarantees me optimum control of post without sacrificing the ability to edit properly. Once you get used to it, it becomes automatic. The Iclone switcher is a great idea (and very handy) but it's just a switcher. Editing usually involves disrupting the time-line with overlaps, and jump cuts.
Just my 2 cent worth.
--Bex