If your current upgrades/modifications are reversible (no drilled holes anywhere, not cuts in sheet metal, all original components in labeled bags and boxes) and you actually plan to reverse them to restore the car to "spot-on factory stock" for a big dollar sale one day, then yes! Make him do them over or sell them and have them done again.
If this is not a realistic possibility, or maybe even impossible, and if you plan to own it forever, and you plan to drive it, then leave it. Because the grain looks better up and down anyway.
Why did it take 3 months? My guy (local guy 2 towns away) made mine from scratch in only a few hours. Dropped off my interior in the morning and he called me that afternoon to take a look at them.