Fix is up for both issues (1.0.9). Thanks a lot for the investigation, it helped me locate the bug quick!
Not taking the nav computer shouldn’t soft-lock you, it should just keep reappearing if you use the Sector Scanner until you pick it up as it’s necessary for progress. I’ve drastically reduced the amount of post-processing it applies, so it should now work both in new saves and any old ones where you already have it.