Yes, this is a major pain
SuperSuite is nice in concept, except that there is no option to install all of the extensions at one time. And updates aren't handled cleanly as stated above. Adobe may be the one that controls the pop-up messages, but WA could do much better in the way it handles the extensions themselves. For example, would it not be possible to run a pre-install check that would say, IF XYZ.mxp exists, THEN don't load ABC.gif? The fact that extension updates try and reload existing, unchanged files is beyond explanation.
If you want to give additional value to the Suite, it would be good to treat the extensions as if they are actually expected to be installed on the same system at the same time. Every time I install an update, I think that much less of WA. This really does need to be addressed. Oh, and that is separate from the frustration that I paid $400 more for SuperSuite than the going price. Thanks for that too, by the way.