Since you are talking about the
build-files.zip, I assume you have either read my blog post and made those changes, or are using the DXA Java private beta.
In any case, be sure to read that blog post and this one, since they give valuable insight to how DXA uses Node.js to build the HTML design. You will also want to read up on Grunt and how Bootstrap is being build.
What you need to know more is that we build the HTML design to be able to publish the HTML design assets mentioned above. The process to build these is Grunt (executed via Node.js) and the outcome is published as binary variants via the
Publish HTML Design TBB.
So you will need to change that TBB, and also make changes to the
build-files.zip for sure. Or maybe you can forget about the
build-files.zip and make all your required changes in the
Publish HTML Design TBB (that depends on what you exactly need to do). Oh and lets not forget that you will also need to change the
html-design.zip, since you want to replace the less files with saas.
Last remark, if you are also thinking about changing the HTML from our Bootstrap design to anything else, then all the views will need to be changed too. Its not something unthinkable, or impossible, as long as you are aware of everything you need to change.