To my knowledge the capsule was constructed with special equipment for the Tokuiden. What this is or how it works I don't know, but the Emaan seem to have advanced know-how on the Tokuiden and how dimensional mechanics work (since they explained it to Kei long before the Terram came up with a final D-transporter).
My inner fan says that it was equipment to allow them to survive the transition into the orbiting Tokuiden. The fact that Terram scientists sabotaged some of the parts to brainwash Kei and olsen seems to imply this, for if it was just a travel capsule then why would the Terram want to sabotage their only means of restoring earth to it's "proper" terram-only state?
As for passing through the sky barrier- the Orbital elevator seemed to be the only way to actually get through it. My inner fan suggests there was a lot of stress around where the elevator hit the sky, but the elevator was strong/close enough to ground zero to survive. More Mu have gone up the elevator and presumably found out what was going on by exploring it.