There is no difference in the set up process. The difference is in the use - the start up registration is just a set of normally preferred settings that is saved in a registration, so you press it right after start up.
Actually “set up” registration would be a better name, since you can have more than one start up registration. For example I have a set up registration that sets pedals a certain way, selects full keyboard mode and one or two other things. But I have a second set up registration that sets up things a little differently.
Mike