You should always reach out to the dealer, they are the ones communicating with the PS team.
If they can not get you an answer you should run away with your money and find a dealer w/ a closer relationship with the PS team (Paul Miles).
That said, stained fretboard is a substantial upcharge and it's unlikely they would stain it for you for free.
I did 3 builds so far and I've never had real communication issues with the PS team through my dealer (Moore Guitars).
The answers have always been prompt, typically within a day or less.
I've been a lot less successful with another dealer recently when I was planning a new build but that was that dealer's fault (too busy).
Out of those 3 builds only one had an error: satin headstock instead of gloss headstock.
They can do it but do not recommend it; they just didn't catch that on the spec sheet and when they painted the guitar.
However when we noticed it we got a reply from Paul Miles, within 30min max, explaining it was their mistake and they offered to respray either the headstock in gloss or the entire neck.
Decided to first receive the guitar to see if the satin headstock would bother me; it didn't and I kept it that way to save a good 4+ weeks of transit + finish work.
I wouldn't say the communication/process always goes smoothly, but if you have a honest dealer they'll work with PRS to make mistakes right.
As I am (and after all this), if the guitar will have one single insignificant defect I will pay absolutely nothing and it will be sent back to USA in 30 seconds.
Not this ^
I would guess anyone on the PS team reading this would not be especially motivated to give a damn.