Being independant and mainstream are not mutually exclusive. Rolex is as mainstream a watch company as you will ever find as they are a household name the world over, even to people who wouldn't know the difference between a quartz or automatic watch if their life depended on it, but they are still independant as they are not a publicly listed company and have no external shareholders.
Breguet is not mainstream (outside of watch fans) but they are not independant either as they're owned by Swatch.
'Independant' in this respect is merely a catch all term that includes smaller brands who are owned by the company founders - small enough to retain a personal and individual touch for each watch and customer dealt with. Rolex might be 99-100% in-house manufactured but if you email them and request a manual wind Submariner with a red dial you're unlikely to get a response, let alone the watch you want. If you email Habring requesting one of their watches with variations of their standard spec you are likely to get the watch you want, even if the base movement is bought in (albeit heavily modified)
The personal touch is what makes 'independant' different from 'mainstream' IMO