Perhaps I am just misremembering but, has the loading method of site CSS changed? I recently noticed that all site CSS shows up in my browser's developer tool as coming from load.php. It is a bit of a pain because it doesn't help you figure out which CSS page it is on. This can be particularly annoying on wikis that have very long CSS pages; whether it is Common.css, the skin-specific CSS, or both.
Like I said, I could just be misremembering. However, I don't recall having to go through as much effort to find "offending" CSS in the past.
Okay, in that context, I am guessing it is also a result of the change in loading method.
So, to be absolutely clear, what you are saying is that you can have @import in MediaWiki:Wikia.css even if there is other stuff in MediaWiki:Common.css? That would imply that the two are no longer concatenated; which makes sense if they are now loaded using load.php. I guess this is a good thing since it makes more intuitive sense. Also, that complicated flow chart on the CSS help page is less significant.