I'm not sure what were the expectations for 13 Sentinels, their latest games were the Odin Sphere remake which ended up <150k across 3 platforms and Dragon's Crown <300k across PS3/PSV
From the start it was obvious 13 Sentinels had a smaller potential for two main reasons
1) As stated in the article it's a less "straightforward" game to sell
2) They released it only on one platform, with PSV SKU being (rightly so) cancelled later on
Every sign made it clear it had a lower ceiling, the demo release being the especially obvious one, and the good thing is that it's certainly not an outright bomb and that their publisher (Atlus) clearly anticipated it and the game had the right shipment to avoid both shortage (undershipping) and price slashed (overshipping)
The problem is however clear that considering the time/money invested during development they certainly hoped for more than 50k retail in the end, a level of sales they hadn't seen for more than a decade and GrimGrimoire at the PS2 end of life.
The other problem is that 1) and 2) above are not problems inherent to Japan, it will be the same on western markets when Atlus USA West will localize the title so, unlike the Sakura Taisen IP whose immediate future in rather clear as we discussed in the last thread, 13 Sentinels seems poised to stay a one off in Vanillaware developed titles, it was a venture worth trying but it's very unlikely that Atlus, or any other publisher, will greenlight any kind of similar project in form and scope in the near future.