Overloading mouse buttons
There's a lot of applications where Alt + Click and drag does something.
That's one of the two most common 3D navigation paradigms.
As an application developer, I do not want the windowing system to eat any mouse shortcuts that happen inside my client area.
Resizing functions need to be kept to the decorations provided by the windowing system, bevause that way I don't need to know what they are to support them on all platforms.