At the moment, you could use customizr and when the next update is flagged as being available, simply ignore it and do not do the Theme Update.
However, you will also be seeing WP updates coming through too (3.8 is out soon). I've not looked, but the 3.7.1 announcement page seems to imply that Automatic Updates is one of the new features. Not sure if you have to set that or not.
Personally, I would not recommend your approach as updates not only provide new features (OK, you may not need them) but they do fix bugs, including security issues.
Bootstrap files are included in the core theme as minified code and you do not need to touch them.