First, this question should be asked on the Theme Reviewers mail-list, not at WPSE. If you want official answers, you should use the official communication channels.
But to answer your question in brief: Themes that implement core features/functionality are required to support the core implementation of those features/functionality.
Thus, the requirement to use wp_link_pages() is… a requirement. Note that if you need to modify the HTML markup of the generated pagination links, you can use the arguments passed to wp_link_pages().
Functions that are filterable can have filters applied, but wholesale replacement of core functions does not conform to the Guidelines.
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