No, they don’t. That is normal. And it has absolutely nothing to do with “Fender quality.”
If dots are centered on the board, then they are not centered between the middle strings.
At the nut, strings are not evenly spaced from their center lines. They are evenly spaced from their edges. Therefore, the E and A strings, being thicker than the D and G strings, take up more nut width than do the D and G.
Place the strings so that dots centered on the fretboard run exactly between the A and the D, and you will have a poor playing bass due to inconsistent string spacing. It will be cramped on the lower strings.
When using dots, the only solution to this problem that doesn’t negatively affect playability is to initially install the dots cheated toward the treble side of the neck.
It is indeed common that necks are tweaked this way or that right out of the factory. But your bass looks pretty okay based on the pictures.