Quick question regarding saddle setback. I had a bike scan done and the report said my saddle setback should be around 3.25". My question is, how can this be assumed as a general number for all road bikes? Does this number just suggest that on whatever bike I get, I should set the setback around this number?

"Around" being the operative word. Measure the length of 10 different saddles and you get varying results depending on brand and model. Average the length of 10 different mens saddles and you get 10.5". That is likely the value of the constant that the fit computer is using to come up with its results as you enter your various parameters into its formula. And no, the formula won't work for all road bikes, only the ones that have the same exact length of seat and top tube, and stem, etc. that will be recommended when the calculator spits out its results.

So you're saying those results only use a general bike geometry to come out with results.

No. I am saying (surmising) that they use a general saddle geometry to come out with results.

Is this set back from a Perpendicular line thru the BB ? that can describe the seat tube angle
with a seat post it self of no or some larger setback ..