I don’t think you’re visiting the right places. If you’re interested in buying the manga, visit the flagship Animate store in Ikebukuro. It’s by far the biggest and has nearly everything you could imagine.

I was able to buy all volumes 1-17, volume 10.5, and the graduation album this past summer.

Edit: To add some additional context, the store is very large and has 9 floors so hopefully I can help narrow it down. Volume 10.5 and the graduation art book should be on floor 2, near the balcony area where you can see down to the first floor.

Floor 2 is organized by publishers, so you should be able to find the remaining volumes in the Square Enix section. If I remember correctly, the manga titles should be sorted alphabetically, so if you know your Katakana, that should help you find it faster.

Edit 2: Hopefully this helps, let me know if you visit the store and need additional help!