I would like to use the master branch of my repo as the source for my github page. I need a build step (ng build --prod --aot) to generate the index.html file that would need to be displayed. I also don't want the generated files to be versionned. Is there a way to accomplish that using Github alone or with Travis CI or any other tool?
You cannot add a step to the build process on the github side. The process that takes your repository and turns it into something servable can only be controlled by the setting on the profile page.
In the end, if the index file is not jekyll, it will be served as is from the repository.
The one thing you can do is have two repositories - one of the "source" and one that is the actual pages that are served. That at least will keep the index.html file out of the source repository.