The only difference between the Atomic and X-Fractor cards is in the pattern of the refractor. I think the only reasoning behind adding any number of refractors to a set is a cash grab.
The Chrome sports cards usually have an embossed serial number stamped in them (1/1, 01/50, 01/199) but for whatever reason, outside of the superfractors, the Garbage Pail Kids Chrome cards had nothing stamped.
One of the collectors at the Garbage Pail Kids Underground Forum posted his Story Heather Chrome collection, this may give you an idea of the difference of the patterns.
Top
Superfractor, Gold, Prism, Atomic
X-Fractor, Refractor, Base Card, Pencil Art
It's hard to see in the picture, but the X-Fractor design has a checkerboard type design.
The Chrome cards are certainly nice when they are in hand and the card stock is certainly high quality. But once I got over the "oooh shiny" factor, I kind of felt ripped off as I've purchased the same card design a few times over already.