Not sure why this article (or Palantir) is trying to paint this as a new thing. I started at a legacy defense contractor immediately after graduating from undergrad. I was hired and had my security clearance process initiated during the fall of my senior year. Unfortunately this was during the great backup of ~2016 so I still wasn't cleared by the time I started, but they still had unclassified work I could do.
You should never submit an SF-86 before your first day of work. That is used to trick you into an interim clearance review that can lead to the job being revoked before you report for work. Once you're an official employee you can't be fired for denial of clearance, though an effort at constructive dismissal will likely ensue if they can't find an uncleared role for you.
Not trying to doubt you, but I find the idea that a company can't terminate an employee for failing to get a clearance for a job that requires a clearance to be tough to believe. You have a source?