Bower always “installs” every project’s files. Including src, build, repo websites, etc. That said, not all of those files go into the final main.js and main.css files, and therefore have no effect on the size of your project.
Deleting lines referencing Bootstrap JS from that file will keep those files from being compiled into main.js, as @austin said.
If you’d like to customize what scss files to include I recommend that you copy Bootstrap’s _bootstrap.scss into your own styles and @import that into main.scss (you can remove it from bower.json). Personally, I do this with a good amount of my projects.