If you build to sell it (and for lots of people the hobby is the building) then it'd pay to do the best you could to get close to stock/correct.....
However, for your own car where the point of the exercise is the enjoyment of ownership....then suit yourself...anything less would be to short change the enjoyment you'd get from the car....there would always be the "I wish I'd built it X way" feeling after you're done.
Personally, I always prefer a car with a "factory" feel to it, but with performance mods and maybe a personalised paint scheme/colour....rather than stick with a dead correct stock car.