This is a limitation in the DITA Open Toolkit that we ship (version 1.4.2.1 is included with XMetaL Author Enterprise 6.0)
There is discussion of it having been addressed in a newer version of the 1.5 DITA OT that we plan to include with our next major release of XMetaL Author Enterprise.
Please see:
http://dita.xml.org/wiki/plans-for-the-dita-open-toolkit-pdf2-plug-inThe argument that needs to be enabled in the DITA OT in order for draft-comment to appear in PDF output is "args.draft". XMetaL Author Enterprise will pass this argument to the DITA OT when you check the checkbox in our UI, but the DITA OT does not do anything with that argument when producing a PDF.