Bootstrap - the downloadable zip file on their site, is great when you need to quickly get a site up and running for a demo or presentation or whatever.
Past that, for pixel perfect sites or something a bit more custom, Bootstrap can be / must be customized. You can do some of this via their config util on their site, but more so via their scss files (whatever their using now) such as adjust column widths, breakpoints, padding, color, etc...
Further to point 2 - if something has specific needs such a multiple part images or layered images - don't use bootstrap. You can use custom HTML / CSS for certain aspects of your site and then use bootstrap for the parts that are more standard.
This of course comes down to how good the developer is. You need to recognize when to use a framework and when not to. Just because a few pieces of a site aren't a good fit for a grid system or a framework, doesn't mean that system can't be used; it just means it can't be used for those parts.