I thought 25.121(b)(1)(i) was clear and did not need an explanation. The minimum gradient of 2.4% is at the point where the landing gear is fully retracted, but without ground effect and in still air. At the maximum weight limited by 25.121(b), with one engine failed at V1, the height at the point where the landing gear is fully retracted is usually less than 35 ft.
Obstacle clearance must be shown with the net takeoff flight path data. The takeoff flight path takes ground effect and wind into account, as well as the variation of thrust with altitude, and the time limit for using takeoff thrust. So the flight path gradient will usually reduce with increasing altitude.