1. Could a tech, or someone in the factory, have possibly dialed in this bass to my high standard and playing preference the way I did? Or could they realistically only come so close?
Unless you are able to tell them REALLY specifically, no.
If you were able to tell them: perfectly flat neck, Use abc brand 25-150 string, X" at 12th fret lowest, Y" at 12th fret highest string. Then front pick up x" from middle string, rear pu y" from highest, x" from lowest..
Also "low action" might require:
Cutting the nut deeper (if they have a standard nut they use, this would require manual work).
Depending on the standard bridge (Fender's tend to bottom out pretty quick) using taper core strings.
Possibly shimming the neck.
And also the quality of the fretwork has to be much better than setting up for the standard ham fisted player that won't notice these things.
Most all factories (large scale facility) are never going to do that. A custom builder will.
A factory will set up each guitar the same way every time with +/- variation. The person doing the set ups does it the same way every time in order to push as many per hour as possible out.
In the time it would take to have the tech read and understand the requested specs, set up to those measurements that person could probably have sent out 3-5 standard set ups. Assuming that tech is tasked to push out X per hour, they would not be very motivated to make that happen..
Then, the next person down the line (assume the "final QC") guy is now going to be bogged down by reading and trying to interpret the requested specs, verifying the setter upper's work and now trying to judge if it passes.
What if it is set to your specs, but the final QC guy plays it and it buzzes (he is an aggressive player or is used to playing 100 guitars all day that feel pretty much identical) does he send it back as defective or let it go?
Generally, this is going to be far too much labor, time and judgement than a production line allows for to be cost effective or viable. This is also why many have "custom shops".