My favorite “feels natural” thing on Apple keyboards was putting raised dots on D and K, on the Keyboard II and Extended Keyboard II. This goes under the middle finger, just like on the numeric keypad.
Eventually they relented and put the dots under F and J like the rest of the PCs.
Putting the Caps Lock key above the Shift key came from typewriters, where it was a "Shift Lock" key (it physically locked the Shift key below it in the pressed position). If you have to blame something, blame typewriters.
Eventually they relented and put the dots under F and J like the rest of the PCs.