Good points. Here are some other points to consider.
Most pedal builders want to keep the stomp switches and control knobs as far apart as possible for obvious reasons. If you try to keep a low profile enclosure (thickness of the box from the pedalboard surface) with top jacks, you may have to move control knobs closer to the stomp switches. Some builders will go with thicker profile enclosures to keep the jacks on top and to keep the controls away from the stomp switches... some do not like the thicker enclosures or the thicker enclosures interfere with their pedalboard lid. Some builders will use longer (larger) enclosures to keep the profile (thickness) low with top jacks, which kinda defeats the compactness goals of having top jacks.
Some pedals have two stomp switches placed near the corners of their enclosure. If adjacent pedals also have stomp switches in the corners then they could be too close to operate without a hassle if they are butted up against each other. So top jacks on these pedals wouldn't have given you much since you may have to space them apart anyway.
Everything has to be a balance of compromises and no design will satisfy everyone's needs.
That's why pancake plugs are so great!!
-Frank