Unfortunately (for me) drupal_goto is urlencoding taxonomy URLs. Leaving ugly URLs for the user. Though they work all the same.

Is there a method of not encoding a URL in drupal_goto for a specific URL?

The closest thing I could get is trying to _goto with the query string:

drupal_goto('', 'q=taxonomy/term/1,2,3');

I find this an odd solution as it works because its assuming a clean URL. The culprit is drupal_urlencode wrapping itself around rawurlencode.

Within the _goto function, there is use of custom_url_rewrite_outbound(). It seems I may be able to use tihs, though I'm not really sure.