I've noticed I'm always the "party pooper" of these topics but here I go again (sorry if my opinions bug you guys):
I think there is way to much read into the story. Something more diabolical? I think they will just think of a new place to stick Sam, like the largest daycare in the universe or some sort of Vykker hospital or something. Going back to places like Rupture Farms having hidden underground breeding centers seems a little to "messy" and plus I think Oddworld doesn't have this kind of "comic book plotline/mystique".
It may seem like I bash the plots of Oddworld when in fact the FMV's and story are my favorite parts! From a storyteller's point of view, I think Lanning-san has a very good idea of what direction the plots are going and ideas for people and places but he doesn't have everything mapped out and pretty much makes it up as they go along (understatement, yes).
Well that's my two moolah
peace