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The documentation says that the text after the > is parsed just as if you had typed it into the project cell in an OmniFocus row, but the behavior described in the documentation and the behavior I'm observing do not appear to be identical. I've filed a bug report, and you should, as well: use Help→Send Feedback to do so. Until the bug is fixed, it appears that you cannot reliably work with identically named projects in different folders via the Mail interface.

The start date, no due date case is easily handled: just leave the due date portion blank (still need the #, of course).

buy milk #today #

would create a "buy milk" action with a start date of 12:00AM and no due date.