Some of the pages would have back end code provided by a PHP callback, XenForo will have full control of that, as ever.
The front end of the pages would still be templates in the template system. XenForo will have full control of that, as ever.
Nothing really changes. If we modify templates, they will become outdated if changed by XF. If we modify the original code, that will be overwritten. If we change the page so it calls different code, then the changes won't apply. But none of this is particularly different from how it works now.