@Dr-Sassi Ah yes, sorry, that nodes modifier is the one that Dominik created and has available for download. It's basically what he built in the video you linked, but with lots of built in options and parameters all packaged together in a single modifier. I would imagine the same problem would happen because I think what's happening is the 'explode mesh islands' is seeing the geo of the inside cube and the outside cube in my nodes mesh I created, and since they are not actually connected geo, the explode node is seperating them and and those are getting iterated.
Using modulo to only use odd or even iterations sounds like it could work because I think I essentially just need the iterations to skip 1 every time, so it would take iteration 0,2,4,6... etc.. That being said I'm new to nodes, and I'm not very proficient in Xpresso, so I don't have the knowledge to implement this idea. I'll do some searching in the manual.
Thanks for your help!