You’re introducing two new intuitions, and it’s not intuitively obvious how they are related to each other. Why would work correlate 100% with caloric intake, and caloric intake 100% with kinetic energy?
Certainly, ‘work’ is highly counterintuitive. If I move a concrete block over loose sand on a beach, I’m doing zero work, in the physics definition, so moving it over a kilometer should be as easy as moving it for a millimeter.
Even ignoring the difference between caloric intake and caloric expenditure, it also isn’t intuitive to me that caloric expenditure is independent of the speed at which one lifts an object.
In the end, the answer is “because the math works out that way, and kinetic energy is a useful concept”
The fact that your muscles burn ATP just fighting gravity is a feature of biology, not fundamental to the physics involved.
If you want to read about another similar example, Google for rocket launch gravity losses.
Stacking a weight on top of a table holds it at a fixed height and requires zero mechanical work.
The failure in intuition here relates to physiology and the mechanism by which muscles work, not physics. Myosin and actin are constantly cycling through bonding and release during muscle contraction, as this is how the shortening action actually occurs. In fact, muscle contraction is particularly unintuitive because people frequently consider ATP the "energy currency", yet the ATP-consuming steps are actually the release/relaxation and preparation for binding, not the pulling action. This is also why the phenomena of rigor mortis upon death occurs.
How I got banned from some reddit channel. Flip this around ask if a ball were fired out of a gun up into the air what height would it reach? A ball twice as fast goes up 4 times as high. If energy is force times distance it had 4 times the energy.