Of all the many variables that Canon has thrown into E-TTL, I don't think the exposure mode is one of them - not as such. For example, if you shoot on Av the camera will naturally adjust the shutter speed to match the ambient, say 1/30sec at f/5.6, but if you make those same settings in manual, you should get the same result.
However, if you decide you want the shot to be 100% flash and set the shutter speed at max x-sync in manual, that will change how the camera interprets the scene and will adjust the flash output, as it should do because the ambient element has been removed - maybe not by much, but it's certainly a potential factor.
I use both Av and manual. Av is brilliant in a fluid social situation because it adjusts for distance, adjusts for ceiling height if you're bouncing, and the shutter speed will float to balance the changing ambient.
With a more static situation, when you know what you want and need it to stay there, switch to manual on both the camera and flash and everything is locked down. You know it won't change, whereas if you're in any auto mode slight movements of the subject can alter the way the system reads the scene and variations are possible.
In a situation like that, there is no advanatge to shooting on auto. Use auto when things are changing and you'll get usable exposure straight out of the can, a quick tweak and they'll be perfect. Basically use E-TTL and auto modes with flash when you just haven't got time to mess about.
NB, I sometimes use manual on camera and E-TTL on the flash - keeps the ambient background constant but adjusts the flash according to distance etc. Lots of permuations
