To be honest with you, I think the only valid argument in here would be design taste: "that project is using mostly the standard bootstrap design,they don't invest in x yet" and that would be a valid just in half. The truth is there is a lot of projects that, even with different code, they all look the same with little variantions. In the end, it doesn't matter the skeleton, what it matters, imho, it's the service they offer.
Of course Twitter uses Bootstrap—it was made by/for Twitter. However, Bootstrap's defaults are based on Twitter's brand guidelines. That's part of the problem: with Bootstrap 1 and 2 basically every website made with Bootstrap looked a lot like Twitter. Bootstrap 3 alleviates that by encouraging customization and shipping with a flat appearance, but sites made with Bootstrap are still very similar to each other—developers don't customize it, and don't try to change some of Bootstrap's easily recognizable idiosyncrasies.
It reminds me of 2004/2005 when every web app was more or less trying to copy the aesthetics of 37signals apps.
That being said, unless you're creating a service specifically for picky designers/developers, it doesn't matter. 99.8% of the Internet has no idea what Bootstrap is.
(ps: the folks who first made Bootstrap worked at Twitter, but Twitter let them take the ownership of the product with them as they left.)