Given how Sony handled the PS4's development they most likely asked developers what kinds of improvements they would want over the launch system. Given the capabilities of AMD's latest GPU tech and potential of the CPU Zen architecture or some mobile version of that I doubt Neo has the level of performance that the rumors state it to (keeping the same core Jaguar CPU architecture never made any sense when they were shooting to improve hardware performance in general).
The very people that have leaked details about Neo prior to Andrew House's confirmation of Neo's existence have also said that Sony has more than one option for this updated PS4.
Leaks of the RX 480's power consumption and performance tests show it to be capable of 5.8Tflops, running on only 100 watts, so with improvements to the CPU architecture in Neo and incorporating this new Polaris GPU Architecture Sony could easily have a 5.8TFlop system, with at least a moderate improvement to the CPU, if not 2+ times the performance of that part in a system the same size as the launch PS4.
If Sony wants to overclock things and the system's case design isn't set in stone then they could build a bigger box and push for 4K in PS4 level games or maybe 1440p at 60FPS, with the RX 480 and a Zen mobile CPU from AMD.
Sony doesn't have to wait, the tech for this could go into production soon and Sony could still meet a Fall 2016 release window.
Given that Microsoft has shown their hand Sony has nothing to really worry about, especially considering the level of games they have coming this year and beyond, the addition of a new, better device is just another platform to run PS4 games to appeal to an even bigger demographic of people.
