I guess to be safe it makes the most sense to put the transponder antenna in the location under the baggage compartment, as appears to be shown in part F-01484 on page 29-02.
I am also leaning toward the Archer VOR antenna in the wingtip, for minimum drag. There aren't any good VOR antennas that would cover up my drilled part anyhow.
So now the question is what to do about the holes I drilled in F-01479 and the coax cable that I pulled back to that location. Any ideas from the much wiser, more experienced builders out there?