Yeah, you can create a Kentico site based on whatever template, including Bootstrap.
Personally, when I create templates for Kentico, I always start outside Kentico and create pure HTML/CSS/JS templates. At that point, such a template could go in other CMS too.
The idea of how to integrate such a template into Kentico is pretty much the same for Portal Engine and MVC. You have to break the template into pieces and add them to respective places. The main difference is how you do it technically. In the Portal engine, you do most of the work in the Admin interface. In MVC, you do it in the backend code in Razor templates.
While integrating the template in Kentico, in some cases you need to adjust the original template to fit Kentico's markup structure (i.e. in the case of the default Form widget).
A good place to start is the tutorial in the docs.