Cracking the throttle works because you're allowing a larger amount of air/fuel mix into the engine. When you go to start a hot engine, some fuel will evaporate on the hot intakes valves that have been sitting and roasting in the engine due to lack of cooling air/fuel flow and no contact with the cylinder head. By cracking the throttle, you have a larger and faster moving stream of fuel and enough will make it into the cylinders without evaporating to start the engine. As soon as the engine starts running, the intake valves will start to cool off and that problem goes away. So you don't want to make any jetting changes to solve a temporary problem that can be dealt with by the throttle.
On the issue of leaning out the pilots. A warmed up engine doesn't need as much fuel as a cold engine. For example, give the bike full choke when it's warmed up and idling and it will probably die. This is obviously dealt with by the choke for cold starts. So if the bike starts well when cold (likes the richer mixture) and refuses to start when hot (likes a leaner mixture) even with the throttle cracked, that's a sign the mixture is too rich on the bottom end. Since there is no such thing as a reverse choke, you have to deal with it by adjusting the pilots.