The greater part of the star systems in Frontier were definitely procedurally generated. But Braben did a good job coding that procedure as all the generated systems do make sense. There are for example only planets around star-types that can have them according to current theories, so you'll probably never find planetary systems around a red giant, though the odd gas-giant can occur.
The hardcoded systems are most of our immediate neighbours plus most other noteworthy stars, such as Betelgeuse which was the largest red supergiant known at the time (can't say if they've discovered bigger ones since) and the somewhat infamous Beta Lyrae which was the only contact start known at the time. Infamous because the game will crash without exception if you try to enter it.
Also that thargoid ship does exist, in a way. The model for one was flipped upside down and used as one of the buildings in those military bases you can do recon and bombing missions to.
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