Logan, I agree with you 100%, for whatever that is worth. That sub is kind of small, and is probably only a prop. But, I don't think Dharma built a teleportation technology as much as they discovered it, and used technology to harness it's power.
Ben probably can't use the Looking Glass now because that would mean opening the doorway. juliette was the last to go through then I guess the heat was on, but Juliette is probably the last one Ben wanted because of her talents, no need for new people when you can have them yourself.
I imagine a portal like Stargate, not exactly, but something.

Anyway, perhaps the linus' went walking though one of these portals unbeknownst to them, perhaps quickly, and hence Ben was born premature. i don't know, something odd about all the Ben being born thing, it must tie into this somehow.. but thanks for making me seem not so crazy Logan...