#Yes, the jump is the distance from the ground to the bottom of your feet
When you make a high jump, you leap into the air a number of feet equal to 3 + your Strength modifier [...] Either way, each foot you clear on the jump costs a foot of movement.
Intuitively, a jumping distance makes the most sense as the distance between your shoes and the ground but really your entire body is moving the same distance upwards. The rules' language talks of the distance you "clear" and "leaping into the air" both of which evokes the imagery of the gap between ground and shoes. More direct evidence can be found in the following passage:
You can extend your arms half your height above yourself during the jump. Thus, you can reach above you a distance equal to the height of the jump plus 1 1/2 times your height.
So it is clear that body height is not considered when calculating the jump height per the rules.
Trying to get any more granular a ruling than that is way more than 5e's rules are designed to handle.