How did only adding parts that are relevant to the current project become some sort of “optimization”? There is more work to do if you start from someone else’s boilerplate that has lots of parts you don’t want, because you have to actively delete things that you need to replace or just don’t need at all.

In any case, some of the defaults in HTML5 Boilerplate can have real negative consequences if you just use it without fixing them. If your market will be using mobile devices a lot, or tends to have limited connection speed for any other reason, then making half a dozen extra requests before you even start doing anything interesting can have a significant impact on performance. Playing around with viewport settings can have significant adverse effects for usability if you don’t know what you’re doing. That little message about IE8 that isn’t going to show up on the recent browsers your developers usually use is going to get you in trouble with a client one day if you develop a lot of intranet sites and forget to remove it.

Reducing the number of includes in the header is very much not premature optimisation. On a phone with poor connectivity, a single blocking Javascript in the header might cause a one second delay (or longer).