A lot of pagination requires some knowledge about newspaper layout, newspaper design, the functions of newspapers. Probably the biggest difference is scale. People tend to use desktop for newsletters which are basically words and some graphics. I think they're pretty much the same. Desktop was probably the forebear of paginating.
Desktop software is probably easier to learn and work with, at least starting up.
As you get into bigger pages, more detail, then you have to a have more powerful software engine. The specialization comes with programmers, the systems people who design networks and the entire way it works. Some newspapers can have the advertising departments do ads which are then put on the pages so that when the page prints the entire page is on one piece of film. We're getting into things like different types of photography. Instead of using film you'll take a picture, record it on an actual computer disc, then load it into a laptop and send your picture in over a modem and never have to develop any film or be in a darkroom.