"wondered for years why most shooters want their scopes mounted as low as possible"
Due to the loopy trajectory of pellets (especially from my R9 & HW95 springers) the preferred shooting distance needs to be considered because a low scope height does favor the closer ranges and the higher scope height favors the longer distances. When shooting at living critters I strive to make all shots within 30 yards which does work well with a lower scope height.
"My guns are all zeroed at 40 yards"
"I hate to aim under a squirrels chin for a head shot"
"dont mind aiming over"
The issue with a 40 yard zero (for me) is exactly what you're describing, i.e. needing to aim both high and low depending on the range. I zero my .177 springers at 30 yards which gives me a "crosshair on" aim from about 15 yards to 35 yards with a slight midrange rise of about 1/4" above the line of sight at about 25 yards (depends on the tune level). With my setup I only need to be concerned with aiming on or high, never have to consider aiming low. Here is a target I shot checking out the trajectory of a certain R9 tune. The target consists of 165 consecutive shots from "bucket and sticks".........
As you can see, aiming at the center of the bulls for all ranges the poi at 20 & 25 yards was about 3/16" or 1/4" above the aim point with a 30 yard zero. Even at 50 yards the pellet drop with a 30 yard zero was only 1 1/2" low.
Anywhoo....I personally prefer having the trajectory "flattened out" at the closer ranges where wind has less influence on the pellet rather than setting up my springer to favor "lottery shot distances".