Because they want you to start at a higher trim. Notice the 5k difference for the two door and four door base? The 2 door price is only to be competitive with the base wrangler pricing, they don’t want people buying a base with zero options. They would probably prefer not to sell any two door...
That is a terribly simplistic way to surmise cost differences. It’s not like they’re just throwing 6 injectors in the glove box dude and looking for more money.