The problem with the bicycle kick is that a lot of the energy you are expending is flexing and extending your joints without causing your fins to "bite" into the water at all, so it isn't driving you forward. The difference between the bicycle and standard flutter kick is that, in the flutter kick, you keep the leg mostly straight, so all the force is transmitted to the fins. The problem with the flutter kick is that it directs the water off the fins pretty much directly downward, even if you are horizontal; if you are tilted at all up, it's even worse. The water coming off the fins goes downward and hits the bottom and can cause fine bottom materials to "explode" up in a cloud of silt.
The modified flutter, which is done with the knees kept bent and the feet above you, is a small kick which moves far less water. Some of that water IS directly downward, but from above your body and therefore further from the bottom. A delicately performed modified flutter will not disturb the bottom sediments very much. A well-performed frog or modified frog will disturb them even less, because the act of bringing the bottoms of the fins together behind you pushes the water out BEHIND, rather than down.