Custom post type query with taxonomy

Answering your second question – yes, it is possible, you can use tax_query for this, for example, this query will get all posts that has any term of ‘flowers’ taxonomy AND ‘colors’ taxonomy:

$query = new WP_Query( array(
    'post_type' => 'custom-post',
    'posts_per_page' => 5,
    'order' => 'DESC',
    'tax_query' => array(
        'relation' => 'AND', // it is also possible to use OR
        array(
            'taxonomy' => 'flowers',
            'operator' => 'EXISTS'
        ),
        array(
            'taxonomy' => 'colors',
            'operator' => 'EXISTS'
        )
    )
) );

The second query will get all posts that have terms from ‘flowers’ taxonomy, but not from ‘colors’ taxonomy:

$query = new WP_Query( array(
    'post_type' => 'custom-post',
    'posts_per_page' => 5,
    'order' => 'DESC',
    'tax_query' => array(
        'relation' => 'AND',
        array(
            'taxonomy' => 'flowers',
            'operator' => 'EXISTS'
        ),
        array(
            'taxonomy' => 'colors',
            'operator' => 'NOT EXISTS' // <-- Take a look at this operator
        )
    )
) );

The code is not tested

Here are also links to the Documentation, check out how to use WP_Query https://developer.wordpress.org/reference/classes/wp_query/#standard-loop

And also WP_Tax_Query https://developer.wordpress.org/reference/classes/wp_query/#taxonomy-parameters