Well, after a study of the windows, I think I've got some good options. There's a hidden trough that runs the full width of the window and is 1.5" deep and about 1" high. There are a couple spots where I've got about 1/2" vertical clearance to squeeze in a sensor (Option A in the pic) and a spot where I'd have a little more clearance than that (Option B).
My first choice would be to place it at the "Option B" location where it would be hidden by the metal bar which is like a piece of angle-iron, so not only would it hide the window-mounted portion of the sensor from view, it would also provide a metal surface to attach to without endangering the window seal.
Given the space, it seems like the "strip-type" sensor might work better than the stubby kind since the cavity is so deep. However, I'm still puzzled with how to affix the magnet to the window. The strip-type sensors seem to be designed to mount on surfaces which are in the same plane whereas in this application the bottom of the sensor would face downward but the bottom of the magnet would face outward. If I install it this way will the magnet still perform well enough?