Hmmm? I would have thought that a merged and split set would take up the same amount of space, considering the fact that no files are being duplicated. Beyond that, an empty zip file takes up 0KB. As a result, I would guess that spliting a set would simply remove files out of the parent zip and transfer them into an empty zip.
you're correct. This is my inability to remember at work. this is straight from cmpro tutorials:
Non-Merged Sets = Any files created will have all of the roms it needs to run
Split sets = Any files created will have the roms it needs as either a parent or clone rom file.
Merge Sets = Any file created will have the parent and clone roms in it.
I think the wording for all of these is absolutely terrible, which is likely why I repress it and then spew half-truths.

What I like to do is a full on, NON MERGED set, where in the end you get 1 zip file is 1 game.
Then I do up my lists, move the files over to the machine, then merge them back together to save the space.
(in all honesty, I don't actually re-merge the sets because in my case, space is cheap and my machine can't play more than a few gig worth of games anyway)