OK, apparently my post didn't make it too clear.
Open mIRC, and open another program, like notepad.
in mIRC, type:
//window -dho +L @Foo -1 -1 100 100
With the window open and on top, position notepad so that the window is covering part of it. Then, in mIRC, type:
//timer 1 10 /window -u @Foo
Before the timer triggers, click on notepad in the taskbar, and do NOT minimize mIRC. You should see the timer expire, which would cause @Foo to lose its "on top" property. However, it will remain the topmost window until another window is activated.
Now, let's say the flag I want is /window -j.
Then the timer above would become:
//timer 1 10 /window -j @Foo
If you were to repeat all of the steps i listed above, then when the timer expired, @Foo would actually disappear. I know this will work, because I wrote a DLL to do it, and my timer calls that DLL. I'm just requesting that it become a flag for /window since many people don't trust DLLs, and DLLs add un-needed size to simple projects like the one I'm working on.