Since he is not the original owner, there is no telling why it is missing the items mentioned. He may believe it is original paint, but untill someone with the ability to spot repaints (some are real good) puts an eye to it, i would doubt the claim of original paint. Anything could have happened to this car over the last 8 or so years. I used to work at a dealer and know how these things happen. For instance, someone gets sideswiped in his 2 month old 99 GT LE, the bodyshop cant get a scoop or correct rocker moulding, but can get a set from a standard GT, the owner says thats fine, just swap em out. Another possibility that happens is when models cross over at the plant, many times, leftover parts are just used up, there are lots of examples of this kind of thing. So in some rare instance, maybe this car left the factory like this. Likely not because of its spot on the timeline of cars, but id it was one of the first GT LE's, i might believe it. It is apparently a LE accord ing to the vin so thats good.
But if i had to lay money on it, id bet it had a repaint, maybe had some damage on one side that killed the scoop and mldg, there was an available donor to get parts from cheaply (or maybe 35th stuff was unavail) and the car was repaired as best it could be. ive seen it a thousand times.
Decent car, decent mileage, probably worth $7500 -8000 in todays market.