If you're not digging through the source you'd probably think it was a lightly styled Bootstrap site as many of the same tells are present (black top navbar, etc).
However, I think there is some massive confirmation bias at work. If a site customizes Bootstrap and it looks nice nobody credits it as a 'Bootstrap Looking' site, so as a result it is only when the defaults are used that people really pick up on it.
That coupled with the fact that there are many more Bootstrap sites kicking around out there I think has led to the misconception about "Bootstrap Looking" sites.
