Yep this is the truth. The entire mess falls on NoA's shoulders. They didn't want to localize the game, then they localize it and choose to have it only available through 1 retailer and don't nearly ship enough copies.
Technically NoA didn't localize the game. NoE footed the bill for the entire localization as I understand it. Literally all NoA did was the footwork to setup for an NTSC-U release. I strongly believe that they didn't "make it available" through only one retailer.. I really believe that Gamestop footed the manufacturing bill. And hell, I would be SHOCKED if they didn't do so because they saw something EXACTLY like this playing out.
I'd also guess that given that sort of agreement, Nintendo is bound by said agreement on doing their own reprint and sending it to Amazon etc.
tl;dr on this post - Nintendo had no faith in a North American release, made a deal with the devil (I don't really think Gamestop is evil), and now that deal is coming back and biting everyone in the ass.
edit - with all of this being said, I still implore people to go out and buy this. Either grab it from Gamestop or if you want to make a stand grab a PAL version or from eBay/Amazon. Holy shit is this game amazing. Most blown away I've been by a jRPG since FFVII or maybe even Chrono Trigger.
edit 2 - actually the more I think about it, the more I believe that if Gamestop DID foot the bill for manufacturing, that the agreement HAD TO have had something in it about preventing Nintendo to do their own print run of the game. Otherwise it's just an agreement waiting to fuck over Gamestop. "Ok GS, you pay for the first print run for the game, and if it proves successful then we can pay for a normal print run and distribute it through you and all of your competitors!! Sounds great!" Nintendo likely got GS to agree to a small (nominal) amount of copies to be sold through nintendo.com for people without a gamestop nearby, but was probably a condition of only the first printing.