Im guessing the second. Flashing the card would probably be a bit too much for some users, plus it might require additional hardware, if I'm not mistaken.
I was thinking that IF gateway gives emunand to 9.0/9.2 3DS users, they would include their diag tool which is able to read the red card, maybe even write? If we look at the video when they showed us system version it didnt have GW before the number. I'm thinking that they got some way of writing an update to the red card therefore no more need of the blue card.