Meta Box

Yes by doing Peter's suggestion of increasing the PHP setting max_input_vars.

Okay I figured it out. Here is my solution:

// Example URLs (In WordPress settings, set Permalink Structure to 'plain')
// https://example.com/?ess_article_category=news
// https://example.com/?paged=2&ess_article_category=news

function ess_article_category_taxonomy_rewrites(){
    // Setup in Metabox AIO
    $cpt = 'ess_article';
    $cpt_rewrite = 'articles';
    $ctax = 'ess_article_category';
    $ctax_rewrite = 'categories';

    // For Taxonomy Archive with multiple pages
    // This must go before rule for main taxonomy archive page below else it will never get triggered
    add_rewrite_rule(
        $cpt_rewrite . '\/' . $ctax_rewrite . '\/([^\/]+)\/page\/([0-9]+)',
        'index.php?' . $ctax . '=$matches[1]&paged=$matches[2]', 
        'top'
    );      
    
    // Match = CPT / Custom Taxonomy / Taxonomy slug variable
    // Must escape delimiter / with \ so = \/
    // ([^\/]+) finds and returns text in matches array
    // ([0-9]+) finds and returns number in matches array
    add_rewrite_rule(
        $cpt_rewrite . '\/' . $ctax_rewrite . '\/([^\/]+)',
        'index.php?' . $ctax . '=$matches[1]',
        'top'
    );
    
    
}
add_action( 'init', 'ess_article_category_taxonomy_rewrites' );

This article seems to indicate the fix is to make sure the custom taxonomy is registered before the CPT.

https://cnpagency.com/blog/the-right-way-to-do-wordpress-custom-taxonomy-rewrites/

Is this possible with the MetaBox user interface?