It has been my experience that you are correct in your assumption that the average smog technician will not be able to tell the difference between a 2014 manifold, and a 2018 manifold.... Frankly, since I don't own a Coyote powered car, I wouldn't be able to tell the difference!
I smogged a truck with internal engine mods for years. It was fairly obvious to most folks that it wasn't stock, by the sound of the exhaust. It was always within the parameters of the various emissions levels and it passed inspection every time. It seemed like it was a "Don't ask, don't tell" policy with them.
In any case, don't volunteer any information. It's all stock as far as you know... And it is.
It is perfectly acceptable to swap OEM factory parts, as far as California smog laws are concerned. The parts must be manufactured no earlier than the date that the vehicle itself was manufactured.
I'm thinking that at some point, any replacement engine for your car, that is manufactured by Ford, will only be available in 2018-up specs.