A three-dimensional memory device includes an alternating stack of insulating layers and electrically conductive layers located over a substrate. The alternating stack includes a first region in which all layers of the alternating stack are present and a second region in which at least a topmost one of the electrically conductive layers is absent. First memory opening fill structures extend through the first region of the alternating stack, and second memory opening fill structures extend through the second region of the alternating stack. The first memory opening fill structures have a greater height than the second memory opening fill structures. Pocket doping regions extending over a respective subset of topmost electrically conductive layers for the memory opening fill structures can be formed to provide higher threshold voltages and to enable selective activation of vertical semiconductor channels connected a same bit line.