You have hit upon an observation asked by many, and answered by few!
Three aircraft I have flown were equipped with split flaps (Cessna 310/340, DC-3). Each of these aircraft specified the use of the first flap setting for takeoff, when I presume additional low speed lift, but not drag, is desired. My (non-engineer) observation is that there was a small increase in lift with these flap settings, which was probably accompanied by undesired drag. This lift was probably mostly the result of making the best of the ground effect cushion, and moving the center of pressure aft a little so extreme nose high attitudes were not required to rotate the aircraft.
Split flaps are mechanically the easiest of all flap systems, and are very good for creating drag, which the older, simpler aircraft needed. Like many things in aircraft developement, a better way (plain or fowler flaps) was found. Since then, you really have not seen new aircraft designs come out with split flaps in the recent decades.
Pilot DAR