Stephen, I can verify that it does not include unlinked sources when you do not select everyone. I tried it three times, twice by selecting the descendants of two different individuals and once by selecting the ancestors of the home person. I also unlinked three sample sources from people so that I’d have something unlinked on my end, and it did not include those sources in the export. If you play around with this a bit, you may get it to work.

Source: http://boards.ancestry.co.uk/topics.software.famtreemaker/8147.1.2.1.3.1.1.1.1.2.2.1/mb.ashx

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