Just my two quatloos worth, but it's generally agreed that the lighted domes at the top and bottom of the saucer are sensor domes, right?
But in reality, they're just lighted pieces of plastic, just like the lighted rectangles (and windows). And some "windows" are round portholes, not unlike the sensor domes though smaller.
So from this we could just as easily conclude that the rectangles are sensors as windows, since they're all nothing but lighted pieces of plastic on the model, no?
Anywho, I like to think that the four rectangles are small craft access doors with a small bay beneath and an “observation gallery” around, similar to the main shuttle bay/hangar, but that’s crazy, I know.