According to this, that thing that looks like a single coil at the neck is really a humbucker
https://docjgear.wordpress.com/2015/05/ ... -predator/I've never seen or played one so I don't have a clue, but was one of the reasons I questioned what you would do for pups if you built something like this.
The simple answer to your question is that what you want is very doable, but would also be very costly as a one off. Any time you start custom building anything, particularly a neck, but everything else, it gets expensive. For a basic super strat it just doesn't make sense.
It makes a lot more sense to find one of the companies that manufacture bodies and necks and put together something close to what you want - Warmoth would be a start. Another option would be someone like Keisel guitars (the old Carvin), they apparently make their own bodies, including some super strat configurations, and will further customize them to your specification.
https://www.kieselguitars.com/customshop/Last option, as you suggest, is to find a guitar that is close and have it modified - not at all unreasonable.