That is no different compared to how it was before. I will attempt to explain.
If you are using Windows Vista/7 and Aero is off, Window Capture and Monitor Capture will behave the identically, the only difference is that Window Capture does tracking for the window you have selected. If something else covers that window, whatever is in that region will show up instead.
If you are using Windows Vista/7 and Aero is on, Window Capture will only capture the window that you select, even if there's something else covering it. If Aero is on, you should not use Monitor Capture at all unless it can't be avoided, as it will limit your frame rate to something like 20.
If you are using Windows 8, Aero can't be disabled, and thus isn't a factor. Window Capture works the same way as in Vista/7 with Aero on, but Monitor Capture is just as fast as Window Capture due to the updated Desktop Window Manager in Windows 8.