I haven't fully considered this but I would wager that in general the part of the render where the frame is actually written to its output format would be miniscule relative to the actual rendering. I'd expect that any difference would become more noticeable the less actual rendering needs to be done. For example, if using After Effects to transcode then I'd expect a higher percentage of time per frame is spent writing the output format than rendering so any difference in the time it takes to write that output would be more noticeable.
I've heard from at least one AE compadre that image sequences are generally read/written slower than movie files by AE (something about accessing one file vs. multiple files), but that could be out of date information.
If you want to just test the speed of the output module then I'd recommend rendering unaffected footage.
-Darby