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It's a little more complicated than that. The order of the CSS files' loading is always the same, even in the concatenated file. There are two problems I've ran across:
- Admin Tools concatenates and optimises the CSS files. This is not a foolproof process. If there are browser-specific hacks (e.g. an IE7 stylesheet relying on the infamous IE comment bug) these are rewritten. Browser-specific CSS files should always be excluded.
- It seems that some rules have to be in different files for the cascading to work correctly. I still haven't been able to identify why that happens, but I have at least one CSS file in one site which doesn't have any effect unless I add it to the exclusion list and it doesn't use any browser-specific hacks.

That's why we have the exclusion lists.

FWIW, neither JS nor CSS combination is a silver bullet. On some sites both work perfectly, on some other site they cause problems. Ideally, JS and CSS should be combines and optimised "by hand" (manually, by a human who understand what he's doing), given the freeform nature of both Javascript code and CSS directives. Automated tools will try to do the best they can, but this is not always possible. In other words, your mileage may vary.