Background: Based on the answer given to this question: "Skype behaviour in the Windows 7 Superbar" ...you can get Skype to minimize to the system tray (rather than the task bar) by running it in compatibility mode. (red flags going off in my head)

That's the behavior that I want but what does "compatibility mode" do to the executing application?

I am concerned about changing the execution mode of an entire (important) application to a previous generation just to alter the user interface behavior a bit.

So, what does compatibility mode actually do internally? What are the disadvantages, as in "how could the application (Skype) suffer?"