So as an update: by and large, most of Vayra's Sector still functions in .96a (MagicBounty legacy support covers HVBs, the VS random bounty manager works just fine, bounties on the player function as they always have, the PDPRC base spawns as it should, etc) but it appears that something has changed in either core Starsector, Nexerelin or LazyLib, and the colonial competitors (Ashen Keepers, the PDPRC beyond L'Interstellaire, the Stormhawks, the AI Institute, Rimward Venture) never spawn their founding expeditions, no matter how long you wait or what date you set for them to begin. Existing factions will still send colony expeditions, but the VS competitor factions will never appear.
I'm not sure how interested Dragn is in continuing to do maintenance updates, but it's about the only thing obviously wrong. VS does work otherwise, since it never relied on complex tooltips and doesn't require a recompile.
The only other problem, of course, is that the .faction files really need to be adjusted in light of .96's own adjustments to faction doctrine.
EDIT: As one other point: I've always wondered if there's a console command to just outright assign the player a bounty. There's a personal playthrough I'd like to do at some point that'd feature giving my character a VS bounty pretty much permanently until the bounty issuers are "dealt with".