Show only posts which can be commented OR have custom meta field

Lets try the following:

By default, all posts are returned regardless of comment_status, so lets run the main query as normal, that is, query all posts regardless of comment_status.

We will also run a small, but very lean secondary query where we will get all posts which have

• a comment_status of closed

• which have a meta value of not yes

The returned ID’s will then be passed as post__not_in to the main query to exclude these posts

I think this is a better approach because handling SQL which involves meta queries yourself can get really messy, specially when you start adding complicated nested meta queries. Let WP_Query handle the meta_query part for us.

We will still use the comment_status parameter which is supported by the custom filter by @TheDeadMedic in your linked question

add_action( 'pre_get_posts', function ( $q )
{
    if (    $q->is_home()
         && $q->is_main_query()
    ) {
        // Run our secondary query to get the posts to exclude
        $args = [
            'posts_per_page'   => -1,
            'comment_status'   => 'closed',
            'meta_query'       => [
                'relation'     => 'OR',
                [ // Compensate for posts which have the custom field set but not set to yes
                    'key'      => 'show_always',
                    'value'    => 'yes',
                    'compare'  => 'NOT IN' // Get posts which value is not yes
                ],
                [ // Compensate for posts which does not have the custom fields
                    'key'      => 'show_always',
                    'compare'  => 'NOT EXISTS' // Get posts which value is not yes
                ]
            ],
            'fields'           => 'ids', // Return only post ID's
            'suppress_filters' => false, // Allow the comment_status filter
            // Any other parameters
        ];
        $exclude_ids = get_posts( $args );

        // Now we can exclude the ID's we just queried
        $q->set( 'post__not_in', $exclude_ids );
    }
});

EDIT

The above code is now tested and working as expected

EDIT from comments

@birgire has filed a new trac ticket (trac ticket #35601) to enquire why comment_status is not available in WP_Query by default. Lets hope that we will see this incorporated into core in the near future. As soon as that happens, the custom filter will not be needed anymore