Sorry for the replying delay - I missed this message!
You can't change the HTML markup of the site - but as you say, it is pretty standard Bootstrap if you use the Bootstrap theme.
If what you want to do is have complete control over the style of the site, is that if you go to the Bootstrap theme options, you can specify your own bootstrap.css in the Advanced options. You can then completely customise your own look and feel onto the Bootstrap theme.
For example, the Croydon Voluntary Action site does this - a custom bootstrap css on the standard Bootstrap theme.
Joe - Voice Admin