As far as I know, Namco Bandai hasn't said anything about it, but there is this picture of the US Collector's Edition floating around the internet that has a steelcase with it, and it is same one that got added to the Amazon picture.
All first print copies were suppose to come with the art book and soundtrack, but I've seen a few reports of people who didn't pre-order it and just bought it on day one not getting them.
The 3699 isn't a bottom number for the number of copies printed, it is in roman numerals as part of the design along the border of a certificate that will come with every physical copy. The numbered print will be in a hologram sticker in it's own location on the certificate and a matching...
You might have paid under the BTA price before the other games were added, since additional BTA games are added to all previous purchases regardless of whether the were over the average price or not. Bastion was the only initial BTA game from Bundle V, which would explain why it is the only one...