Beat the game last night, rank 6, got all the bunkers, found all the areas (i'm like... 80% sure on that one).
I still don't have the achievements for Rank 1, getting the command module, visiting all regions, or scanning a ghost (at least, i'm pretty sure that was a ghost?).
Here's the output log: https://pastebin.com/21BBWbiP (although it didn't look like it contained anything pertaining to Steamworks, but may as well attach it just in case).
Fantastic game, though.