How would I format a query that depends on post parent taxonomy

You can still use get_posts:

$parents = get_posts(
    array(
        'posts_per_page' => -1,
        'post_type'      => 'my_custom_post_type',
        'fields'         => 'ids', // Just get IDs, not objects
        'tax_query'      => array(
            array(
                'taxonomy' => 'my_custom_tax',
                'field'    => 'slug',
                'terms'    => array(
                    'foo',
                    'bar',
                ),
            ),
        ),
    )
);

$post_ids = get_posts(
    array(
        'posts_per_page'  => -1,
        'post_parent__in' => $parents,
        'post_type'       => 'my_custom_post_type',
        'fields'          => 'ids',
        'meta_query'       => array(
            array(
                'key'   => 'my_custom_field',
                'value' => $foobar,
            ),
        ),
    )
);

Further reading on tax queries and meta queries.

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