A semiconductor structure includes semiconductor devices located on a top surface of a substrate semiconductor layer, lower-level metal interconnect structures embedded in lower-level dielectric material layers, source-level material layers, an alternating stack of insulating layers and electrically conductive layers overlying the source-level material layer, memory stack structures, a vertically alternating sequence of insulating plates and dielectric material plates laterally surrounded by the alternating stack, an isolation trench fill structure interposed between the alternating stack and the vertically alternating sequence and including a trench fill material portion and a capping dielectric structure overlying the trench fill material portion, and a first through-memory-level interconnection via structure vertically extending through each plate within the vertically alternating sequence and contacting a top surface of one of the lower-level metal interconnect structures.