In my opinion, the Builders created the pocket universe as sort of an ark to repopulate the Universe after some on-coming disaster that they knew was coming. Plus, I think the Builders (or the last Builder) knew they were about to go extinct and that's why they left the Pylons and Skylons to keep the program running after they were gone.
Another thought that occurred to me, since time is so weird in the Land of the Lost, is that perhaps the Builders were the last beings to exist in the Universe sometime in the far, distant future.
If you wear this afro, your punch will become stronger!
I was always under the assumption that the builders had been Enik's people (the Altrusians), and that they didnt become extinct - war had sunk their race into barbarism, eventually evolving into the simple Sleestak.
David Gerrold once said that the LotL acted as a "cosmic way station" constructed by the Altrusians for beings travelling via the dimensional doorways. So presumably one intentionally entered a dimensional doorway from one's own time and place to get to Altrusia. From there, another portal could be opened to go to another time and place.
With the collapse of the Altrusian civilization, the entire system went haywire since the Sleestak no longer had the knowledge to use - much less maintain - the pylons and matrix tables. Enik at least had knowledge of how to use the equipment, but the dimensional doorways were glitchy to say the least (best exemplified by the Marshalls' paradox as seen in the Circle episode). S'latch also seemed to have inherited this knowledge through some freak genetics, but his fate was unknown. The Skulls in the Library of Skulls were also a conduit for the ancient knowledge of the Altrusians, but unfortunately the Sleestak often asked the wrong questions or misinterpreted the information presented (it didn't help that the Skulls often answered in riddles).
I had always assumed that the Sleestak leader (introduced in "Blackout" and featured prominently in season three) was a partial S'latch-like mutant, inheriting a minor intelligence allowing him to speak English, but barbaric enough for the Sleestak to accept him as their leader.