No, if I go through FCP > AE > FCP, the original FCP footage will look the same as the rendered AE footage in FCP. HOWEVER, when the footage is loaded into AE, AE adjusts the gain so that the image looks lighter in my reference monitor.
In other words, the gain information that the two programs send to my firewire reference monitor is inconsistent between the two programs.
If I enable Match Legacy Settings (or use an older version of AE), AE eliminates this problem (adjusts the gain to the reference monitor so that it displays the same as it does from FCP) – but I lose the advantages of working in an entirely color managed workflow.
Also, in relation to your comment on input profiles. Are you saying that for footage that has an embedded profile of sRGB that it is better to change it’s input profile to SDTV? Depending on where the footage comes from (the internet, for instance), wouldn’t this result in a less accurate color conversion to the SDTV working color space?