Makes sense. There are quite a few flex libs that get left out if you go with the pure actionscript option.
You pretty much miss out on anything you might have wanted from spark and a number of the classes that leverage mxml approaches to the visual side.
By now I'm guessing you have already researched and found the classes you were missing and wrapped the code to not use them, but perhaps someone else clawing out their eyes will appreciate knowing there is a fairly big difference in what IntelliJ excludes when you toggle to "pure actionscript".
Of course the AS3 documentation won't really cover that AFAIK because the intent is that you will use both mxml and AS.