They are embedded in my FTM file as much the same way as you'd embed a private photograph. Haven't you used FTM? You must to now what you stated. Those files can be used in other ways outside of a FTM file you know.
Those programmers can easily distinguish between one's own tree and other users' trees for non-subscribers.
That type of business decision is doubtless why many people make their research private when done with it. Why reward Ancestry.com with your work when they won't let you view your own information online unless you pay a subscription.