It isn't secret hardware in the pipeline, it is the pipeline itself that is different. Unified RAM, cache scrubbers, priority I/O beyond what is being used elsewhere.
To say "The APU is the same, therefore the system arch is the same" is either disingenuous, or completely lacking in comprehension. Even if the APU in the Series X is faster, if the BUS isn't providing the data as quickly, it is bottlenecked.
Imagine two 10-storey buildings. One has an elevator that goes from the top to the bottom, the other has two separate elevators, each covering half the height. Even if the 2-elevator building has bigger elevator cars, it will take longer to get as many people from the ground floor to the top floor, due to having to change elevators.