When we download a free template (e.g. ASP.NET Core + jQuery), the default setup sees both Bootstrap and Materialize on the same page. The two frameworks have conflicting class names.
Is it assumed that we will comment out one or the other?
No, you should not comment out either.
The free template uses AdminBSB, which is based on both Bootstrap 3.x and Materialize.
Since it is a free template, you can replace the theme yourself.