Actually, it's more organized to have an array, json, xml, whatever, to setup the levels and just one layout to read that and build the level. Also, having all loadable objects on a separate layout allows you to only create the ones used on that level specifically, there's no burden whatsoever in this model dop2000 is explaining...
This is not, or at least shouldn't be, a strong minority. Several games would be better implemented if they used this framework. If the majority doesn't, it's not because it's better, but because the majority is probably not skilled enough to do it properly, I guess.
Finally, let's suppose you created 100 levels and noticed, later, you must make some change on level structure that would affect every level. With the multiple layout setting you'll have to make this change 100 times. With the other approach you only change once.