Its a delicate balance between the needle diameter, slide cutaway, slide height, float height, air screw, and pilot jet. They all have to work together to get the bike to start easily, not load up, provide instant throttle response, idle, and run smoothly and cleanly. There are always compromises in one area or another.
By lowering the slide you ensure you are on the needle straight, and isolate the circuits more which results in less inconsistancy.
You'll never jet around a mechanical condition such as air leaks, worn reeds, low compression, large tolerances, etc as well.
If a bike idles well in neutral but not so well in gear its usually due to a bit of clutch drag. I personally set my bikes so they idle well out of gear when hot, and stall after a few seconds in gear. Setting the idle up results in a bit of pipe bang/surge on closed throttle. Low idle, and good throttle response is what you want when riding. Easy starting too!