Posting just to possibly soften some worry about the preorder ship bug, if anyone's still worried about that. I deleted my save last night for fear I wouldn't get the hyperdrive part.
After playing for a while on my new file, I felt bad I didn't at least investigate further on my original save, so I restored it from the PSN backup. Following exactly what the atlas suggestions were; Open the galactic map, warp to a new system, Scan, it found a waypoint, that waypoint produced the hyperdrive print. I was relieved.
A side note from my experiment, on my old save, every time I would load the game from scratch, after the No Man's Sky splash, the galaxy and stars streaming past would start in a deep lush purple color, and fade around an overall dark pallet until my planet loaded.
When I started a new game, I noticed loading in would produce a bright green backdrop followed by other bright colors. Every time. I then deleted/started again twice more before restoring my original save, and both of these produced the same colors. After restoring my save, I was back to purple.
tl;dr - I think where you are in the galaxy produces a repeatable opening load screen color, (and possibly galactic map coloring?) and I think new saves are created in similar general areas, and as they fill up, new areas are generated.