"but the amount of day-to-day personal autonomy people have over their own work and careers is often less in the startups"

That might be true if you work for a shitty, tyrannical founder. In my experience, a good startup will recognize that they need employees to be relatively autonomous and self-sufficient, simply because the higher ups don't have time to babysit. Startups lack the resources for multiple levels of engineering managers, and therefore shouldn't hire people that they don't trust to be autonomous.