Before we started using MB, I'd been creating a Metabox Grouper class to combine related metaboxes or custom fields.
Turns out, MB has everything I was thinking of adding and more, but it's missing one tiny thing...
When I inserted a standard WP custom taxonomy, rather than create my own drop-down or select, as you've done, I simply called the WP functions:
post_categories_meta_box() and post_tags_meta_box()
which inserts the standard WP interface for adding terms. This has the advantage of allowing users to add new terms without leaving the 'Add new post type' screen.
Could you add another option for the category and tag metaboxes to output the standard WP interface, as well as all the options you have?
Unless of course I'm missing something that would allow users to insert them from the post-new page already?