Thanks @karren_owl --- I found the culprit. q2-phylogeny is using scikit-bio behind the scenes to do the midpoint rooting --- I was reading up on the Newick file format (used to represent the tree here), check this tidbit out:
In this format, underscores are treated as spaces --- in order to include a literal underscore, you must precede the underscore with a single-quote '. You can also surround the entire ID with single quotes.
You can learn more about the format here: http://scikit-bio.org/docs/0.5.5/generated/skbio.io.format.newick.html#module-skbio.io.format.newick