I think part of the problem is that "Purchased" doesn't actually mean the same thing as "Paid for." I suspect it really only means "downloaded." Gotta remember, Apple is in business to make money, despite providing Mavericks for free! đ Even though Mavericks is free, it still shows up in the "Purchases" list. With this possibility in mind, I'd suggest you go ahead and download the "supplemental" stuff (I am assuming it is free, BTW). You should then be able to use the "Purchases" page/screen to control-click that stuff and hide it from further update notifications.
The problem, in my humble opinion, is that not much thought was put into the App Store concept. We (Apple) now has a system designed for purchases which may actually be free. Oops! They then decided this "Store" should let us know when the things we bought/downloaded were updated. "Easy! We'll just create Notifications and everyone will know about the updates even if they don't check email" (which was a fine method 'back-in-the-days, of course). But Apple forgot that people don't always continue to use or even want everything they ever downloaded, even if the paid for it! They then devised a way to hide the methods they use to see what we've bought or downloaded and created a database to keep track of the stuff we dont care about.
Long story short, this is an almost exact description of bloatware. An app starts out doing one thing, maybe even in a great way, then managers start thinking of things it could also do. Some of those new things may not be desirable but they get added, anyway. Eventually, things start interacting with other things and people have problems or the app starts crashing or... I blame this SU pronlem and certainly the iWorks Suite fiasco on many of the managers at Apple who seem to have forgot the basics of Apple's philosophy: Make things work, always, easily, intuitively and beautifully. Nobody said that's easy. You want 'easy' go work for MS! đ