I was surprised to see that Parts One and Three don't influence each other. If the ship took some scrapes or damage as a result of the first Montage Test, shouldn't the scenario give the GM some guidance to incorporate that in the second Montage Test? The "Total Failure" option in Part One says that several ship systems malfunction or cease operation. As a GM, I'd prefer the designer give me some explicit options to choose from that will have some mechanical effect in the second Montage Test involving the ship.
There'd have to be some connection between the physical components of the ship that were damaged or destroyed during Part One and their practical, physical use when navigating the Willy-Wonka-psychedelic-tunnel nature of the challenge in Part Three. For Part Three to make sense, the GM (and designer) need to understand how these timescape/spelljammer ships are typically navigated through astral rifts. I don't need a whole treatise on Timescape Ship Captaining. The mechanical effects described in Part One would be enough.
Why not put some mechanical bite into the Partial Success result in Part One, too, rather than glossing over it as "a few scrapes"? Keep the Victory gains and Recovery losses. Just put some mechanical meat on the dry narrative bone.