I prefer to take the Bootstrap starter template as a “general suggestion”, only using the bits that I need to, and that I know are necessary for my project – typically just the html5 doctype, viewport meta tag, html5 shim, and core CSS.
I don’t tend to use respond.js for IE8, jQuery or Bootstrap js
Neither do I usually bother with the X-UA-Compatability tag. Sure, it helps IE work more effectively, but it isn’t required.
I guess it comes down to knowing when to make use of the tools in question and making a judgement call on a case-by-case basis :)