2.4% gradient is just that. Go forward 100 feet, go up 2.4 feet. Part 25 is simply what the FAA says the airplane must do, no obstruction planes, no obstacles, just takeoff and do this. The gross and net thing is just a buffer between manufacturing and real world ops. I'm sure you have flown two different tail numbers of the same airplane and can see how the exact same make and model can behave differently even on similiar weather days.
The definions of first, second, third, and sometimes fourth and fifth, segment climbs are a little fuzzy at times. First segment is liftoff to either, gear retraction (lever selected up) or gear in the wells, ends at 35 feet above the runway (with most airplanes this will be with lever selection to up). Second segment is from 35 feet above the runway/gear selected up, to some number, 400 feet, 1000 feet, 1500 feet, etc. This is the one everyone gets all spooled up about. It is important to note, absent a runway analysis program, what your second segment data is actually telling you in the AFM. The number you get isn't going to be a rise over run gradient, it is going to be a snapshot of some point along the second segment path, either the beginning, middle or end.
I used to have an awesome PDF from Airbus that went in to this stuff with some great graphics. It is a real eye opener as to what the airplane is supposed to be able to do at max effort takeoff with an engine out.