I guess that is a fairly complex thing for a camera to do, but it would still be nice. So, you switch to manual mode. But with auto ISO there, no EC. So if you shoot the 5D Mk III, you really have to do most or all of your exposure compensation via ISO #. Well not really, but you know what I mean.
While I don't have access to Canon's firmware sourcecode, I'd say this is less "complex" but more like "trivial". But as I wrote, I suspect this and disabling ec on m is intentional, I have no other explanation for it. And this is the reason I almost never use m on my 60d, too - I'm used to quick ec changes with auto iso from the av mode.