How can I add multiple ‘tax_query’ arrays via a loop?

OK, I have no idea how and why your code should work… It has nothing in common with correct PHP syntax… But it’s pretty good pseudo-code, so I think I can guess, what you wanted to achieve…

$tax_query = array();
if ( have_rows('category_taxonomies') ) {
    while ( have_rows('category_taxonomies') ) {
        the_row();
        $tax_query[] = array(
            'taxonomy' => 'taxonomy',  // <- you should put real taxonomy name in here
            'field' => 'slug',
            'terms' => get_sub_field('category_taxonomy')
        );
    }
}

$posts = get_posts( array(
    'posts_per_page' => 10,
    'post_type'      => 'company_product',
    'tax_query'      => $tax_query
));