So, the seating isn't intended to match reality. The seating numbers are derived based upon the certified maximum passengers of a particular plane, and the seating you're allowed to put on it is determined from a formula. The formula doesn't consider what the plane actually had in real life or any other consideration - only the maximum certified passenger count. At some point, real life has to be simplified for the purposes of making a playable game, and quite frankly, I don't want to have to micromanage the number of seats in a row on a plane in my fleet when I'm playing this game for fun.
The only ax I have to grind with how seating configuration is done is that the MD90-30's certified max is the same as the MD80's, resulting in the same number of seats provided by the calculator even though the MD90 has a stretch beyond the 80's in the real world.