Honestly, because practicing in game is too hard and has too many variables. By playing in customs you have no excuses and can accurately gauge how much you are improving because there are no other variables (enemy player skill, jungler involvement, support skill, etc.) You should be able to have perfect CS in a custom game but you will find that doing that is much, much harder than it sounds.
Its just like practicing by yourself for sports. Shooting free throws, playing catch, etc. The best way to improve is to do one thing and one thing ONLY until it becomes muscle memory. That's what playing in customs allows you to do. It removes all other distractions and allows you to focus solely on improving your last hitting.