Hi dave69,
Creating the same file structure will not override or work with the child theme. You need to unhook the function and customize the code. We have replied many times how to unhook the functions.
View this below link we have already described how to unhook
https://www.themehorse.com/support-forum/topic/loading-header-extension-php-in-child-theme/
Regarding to your above questions
1) How do I remove the comments from from pages? (without needing to do it on each individual page)
==> This is wordpress default feature. Before wordpress 4.3 you need to do it manually. But i think now in 4.3 version there comments are automatically off by default.
View this below link
https://wordpress.org/news/
Comments turned off on pages – All new pages that you create will have comments turned off. Keep discussions to your blog, right where they’re supposed to happen.
2) Where is the documentation on the various loops that appear to be available?
==> Which loop are you talking about. if you are talking about the post or page look then you go to the theme folder -> inc -> structure-> content-extension.php
In this page we have defined all the loop.
Hope this may help you
Thank you!