After finally evading the bugs, I can give this game the recommendation I wanted. After blowing away my save and starting over from the beginning, "Withdraw from Independence" finally became winnable. I also restricted the game to one CPU core in case of RDTSC-related weirdness, but that probably wasn't necessary.
Tachyon is a great space combat flight sim. The storyline is fairly compelling, the missions are interesting, and the environments are neat, too, even though it's in space. The Twilight region is appropriately spooky, the lawless fringe has a number of interesting starbases, etc. It's not quite as open-ended as some others of the genre, but it's not all shooting at ships, either. I had a lot of fun with this in the mid 2000s, and I'm having lots of fun with it again.
Details on bug:
Apparently there was some weird persistent bug that caused the full Galspan force to be present in the Independence sector as soon as I arrived. Let me assure you, that mission is a LOT harder when there's a destroyer right in your face as soon as you arrive. Somehow, something I did fixed that, but those shuttles still went down way faster than I remember until I deleted my save and started over from the beginning.