Be a little careful, because I think you're reading a Stack Overflow question recast as a blog post (Spolsky just moved his blog from CityDesk --- can you believe he was still using CityDesk? --- to WordPress, and so I guess we'll be seeing some more stuff like this on it). People are less careful capturing all angles of an issue on forums than they are in blog posts.
I assume Stack Overflow is just like most big software shops, in that if you have a side project you want to work on and be severable from your employer, you just fill out a little form and get it signed by your manager.
You'd be pushing things to take it further than that, but I'll add anyways: if they're like most firms (and I have every reason to think they would be, since they're famously dev-friendly), even if you didn't follow this process, they're not going to fuck with you. It would be terrible for their own business.
But if you're going to take a side project and turn it into a business, it behooves you to do things by the book, because the worst possible problems for a startup to have are the kind that don't become apparent until after your project is successful.
(Also: Spolsky is the CEO of Stack Overflow; Anil Dash is the CEO of Fog Creek.)