A fact that a lot of people miss is that windows does not have a separate window manager component :- most of the window management duties are performed by each window - usually in DefWindowProc.
Most window positioning and activation / de-activation is done - ultimately - via a call to SetWindowPos - which always sends a WM_WINDOWPOSCHANGING message allowing the window to have a final say on what happens.
DefWindowProc also activate its own window in response to mouse clicks and so on.
The result of all this is, it is quite possible to create windows that never accept activation - it does require an extensive understanding of what messages and situations might have led to an activation.
Ultimately I can say that it is VERY handy to have a debugging setup configured for remote debugging - so that you can interact with your debugger without effecting the activation state of the system - and hence drop a breakpoint into the window in questions WM_ACTIVATE handler and simply debug any situation leading to an unwanted activation.
If You want to handle keyboard focus as well, it might be trickier - normally focus is given to an activated window - but again its usually the DefWindowProc responsible for assigning both. I just see it dangerous as having one window, still obviously activated, and another with focus. This will confuse any assistive software greatly.
I'd be tempted to perform a message loop level message hook - Similar to IsDialogMessage - to filter keystrokes intended for the popup window.