I am a UX designer, usability, and visual designer, who makes the wireframes and mockups for developers. I also typically go in and write a lot of CSS and html as a part of the designing.
Presently, I am really in favor of developers using Bootstrap as a CSS and html baseline, and then having the custom design built on top of it.
Even with a designer, I still don't see a tremendous advantage of rolling a entire CSS (or Less) stylesheet. The developers can start building and use Bootstrap to get things rolling, and the desginer can do the hi-fi gloss designs, and then you just change the Less to match the gloss.
So you end up with a less/html template that is very solid, and a custom front end that is a clone of your glossy mockups.
It seems like you get a lot more value and stability from Bootstrap + a designer, changing Bootstrap to match your custom design.
I totally agree that in production, you shouldn't be able to recognize Bootstrap. But if you create your own "skin" on it, I think it gets you moving a whole lot faster, and with a broader coverage of css/less than you may have rolled on your own.
Engineers should be producing elegant, innovative solutions through code, and Designers should be producing elegant, intuitive design and usability through interface and design. No one really needs to reinvent how to set up a blanket CSS and html template.