Half of my top-level window is transparent, except for a few sites.
Do you mean 100% transparent (i.e by using a mask) or only partly opaque?
If its 100% transparent, no mouse events for that widget will be cought where it is fully transparent.
If it is only partly opaque, then you will have probably have to use an event filter.

I want to ensure that mouse events occurring on that half had passed through my application and reach of applications under him.
Do you really mean "application" or widgets?
Or, do you really mean event between applications, or events between widgets (windows) in the same application?