While it is an absurd way to measure it, surely you aren't suggesting that the PS4 version didn't cost more than the 3DS version to make. SE will likely make more of their profit off the 3DS version not only due to sales, but cost to make. Will we ever have solid evidence of this, likely not, but it isn't some fantastical thought that games that require larger quality assets and precision character movement costs more.
I'm not suggesting anything, just got surprised by a funny statement.
PS4 version cost more to make, and also sells for almost double the price, but that's not even the point.
This HD costs wildcard to push arguments has already gotten out of control. DQXI is barely an AAA game if you compare it to the software we see each year on the ps4. It uses a modern engine and modern tools and has a pleasant art direction so it looks nice, but the game is not really pushing anything impressive at all.
The fact that the game has no voices and repurposed music says much more about how it's not a big scale game.
Making a game that doesn't look like it could run on the ps2 does not mean it's a colossal investment that needs a gazillion units sold to break even.