Just piggybacking off the comment made during the discussion about Fan Club Porygon, Now that you think about it, I think the Fan Club Magikarp is rarer not because of the late addition but because there was already a version of Shiny Magikarp released with the Neo3. I can totally understand why it would appeal less to collectors where you already have a similar copy in a prior release. Given how difficult it was to obtain the GET points, I think participants just chose the other two unique cards with the Eevee and Porygon.
Thanks for the discussion.
Cheers!