Facebook, on the other hand, became successful without any of the additional third party applications that use it as a platform today. A "bare" Facebook, without any third party apps, retains quite a lot in the way of functionality. This means that Facebook's interests are much less aligned with yours than Microsoft's.
Yes, it means something. The question is what.
It might mean that Facebook has strong incentive to steal Zynga's business.
Considering there are rumblings that Zynga is casting about for other platforms, Zynga might think so.
If Facebook could be the home of many profitable apps that it had fair and transparent way of taking a cut from, then you could feel like Facebook was likely to keep its ecosystem working. Until then, it seems like anyone building on Facebook is subject to continuous risk of, as you imply, a sea-change in Facebook's operations.