That value is set on a per user basis and saved as user meta. We can intercept and modify it to a fixed value using the filter get_{$meta_type}_metadata
.
Create a Must Use plugin and it will be active in all the Network:
add_filter( 'get_user_metadata', 'comments_per_page_wpse_95420', 10, 4 );
function comments_per_page_wpse_95420( $check, $object_id, $meta_key, $single )
{
if( 'edit_comments_per_page' == $meta_key )
return 999;
return $check;
}
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