Taxonomy term page $content is empty but shows up later
I was stuck on this myself and went hunting for the answer.

From my understanding, taxonomy_term_page generates data for a page. Therefore, the $build variable outputs its content to a page template and that's why you see it after the theme template.

The $content variable in the theme template, taxonomy-term.tpl.php, should contain the description or any fields you have created for the term.