Thanks Brad for checking this out.
I do know that if I add \usepackage{url} I get the same errors you do about a missing \begin document. This makes me think that there is something in the environment or some other option that should be used to make the url package behave with xelatex.
This can't be the case. As I mentioned, it successfully loads without errors when typeset from the command line.
Do you have some TM_LATEX_OPTIONS set in the project where you use xelatex?
No.
There is a bundle command called Configure which also brings up the configuration window, so you don't have to typeset a document to find the Configure button, you can choose it from the bundle menu before you typeset.
Sorry, I missed that.
Best, Mark