As I work with multiple displays, I think you're sugar-coating it to say it works "well." In fact, Apple knows how horrible it is. That's part of the reason they are displaying the full-screen support as a major upgrade with their new OS release. It is currently so bad, that not only do I find myself frustrated, the PR and dev teams at Apple want to shout about their fix from the rooftops.
Exactly what can't be done?
It seems to me that Apple's emphasis has been on using one screen well and applications like FCPX that use privileged APIs to use fullscreen well across monitors, but developers who use multiple displays in more complicated ways are pretty much stuck with third party solutions (I use SizeUp, and I used to use Cinch). This doesn't solve the issue you mention, but I'm very happy with it otherwise -- and when Apple incorporates the features of nice third-party utilities into the OS it gets lambasted from the other side.