I know a bunch of people who work in AAA videogames, and they definitely don't think they have the freedom to experiment once they get too big. It's pretty routine for them to take their golden parachutes and start a little indie studio to do so, once they no longer have to worry about things like paying for their mortgage any more.
No. The big publishers that have HR people and accountants, like Mongoose or Paizo or Kobold or Black Hat and the like aren't indie outfits any more. They have established game lines, customers with expectations of the publishers and their output, etc.
Indie publishers, IMO, are the ones that pop up, do a few weird things and may vanish without a trace. They're likely "based" out of a garage or more realistically a kitchen table and their accounting department is their mad scramble to set up QuickBooks before tax day.
In the traditional D&D-like RPG space, I'd say Cairn or Knave or the stuff put out by Flatland Games are indie and Paizo, Kobold, etc. are not. It takes more than just being "smaller than WotC," which is everyone, to be a small scrappy independent.