I'm not sure exactly what you mean by 'sequence', but to what extent are you able to tell how the area was originally supposed to play?

: As far as dropping the ghosts off unmanned, they probably wanted to give the
: player the ability to take them out before they land, allowing the players
: actions to have more impact on how the encounter played out.

That could be it. You could overturn them or even steal one.

: Grammatically speaking Ghost should be capitalized because it is a name of
: the object

Sure - and I'm assuming someone eventually pointed that out, if it was needed.

: I assume checkpoint was more player friendly than autosave.

Well, it allows a different way of talking, and also it has a military sound and association I think. Maybe these were the reasons they adopted it.

: Something tells me though the first room before the bridge was
: supposed to be different, and perhaps you would have been able to fly it
: through?

The LZ exit passage appears to have the same cross-section as usual though, in which case it would've been an awkward squeeze to get to the first room.