That's a ton of work for something SC *should* be able to do for you.
SC actually has 2 ways to capture aero transparency corner windows.
The first is automatically (enabled by default), which should work fine BUT will not work if the child window is on top of a parent window. solution in your case might be to move the child window off the parent window into a blank area. This is the option on the "Window Capturing 1" tab.
The second is that sc can be asked to automatically fixup round corner transparency by looking for the corner region -- essentially doing what i think you are describing above (check the "Window Capturing 2" tab).
-- you say you are on Windows 8 -- i thought win8 does not use aero transparency corners, and it could cause trouble, so by default SC won't try to do the corner transparency on windows 8.
BUT there is an option to tell it you want it to. Go to the "Miscelaneous Tweaks" tab and enable this: