Looks like in version 2.5 they have finally added this feature. "Ancestor" now actually means "Ancestor" and there is a separate "merge" option
From the command line you can do something like this:
$ opendiff mine theirs --ancestor base
Where "mine" is my version of the file, "theirs" is the version I'm trying to merge with, and "base" is the common ancestor of "mine" and "theirs.
This command will open File Merge and show the ancestor at the bottom (where the merge is in my example from 2010).
Unfortunately, it's not possible to use the --merge option along with the --ancestor option. So you can't view a three-way merge AND use File Merge to resolve the conflicts at the same time.
I am starting to use File Merge for viewing and understanding the conflict, then editing the conflict markers in a text editor as usual. (sigh...)