Pagination on Shifter
Shifter will get paginate link of "Pages" or "Posts", which returns ture of is_single() function, from the result of wp_link_pages() function. Shifter lists up URL should e generated from the result of wp_link_pages() function.
Shifter also generate pagination, if "Pages" have wp_link_pages() function.
In case of the Page with templates which have pseudo-added-page-links.
The wp_link_pages() function will not create page links in this case. You should create paginate link by using filter hook wp_link_pages.
c.f. post-template.php line #L856 in tags/4.9.2/src/wp-includes
sample code
The filter hook is affected on post-template.php line #L938 in tags/4.9.2/src/wp-includes , so use filter hook wp_link_pages .
Here is our sample code:
add_filter( 'wp_link_pages', function( $output, $args ){
// write some code here for modifying $output when the Page.
return $output;
}, 10, 2 );