As much as I enjoy the idea of having official storage solutions, I can see some good reasons why they'd be reluctant to create better storage solutions:
1) It's not very common. Name 5 TCGs that come with awesome storage solutions immediately. Selling card sleeves and deck boxes is very common among card game producers, so obviously they'd do those, but storage boxes are very very far from universal.
2) It adds an expense to the boxes. I think this card game costs plenty enough as it is and if they raised the cost even 1 more dollar, it could drop sales.
3) Do what you're good at. Why do card storage solutions if you're not good at it?
4) Third parties ARE good at it and they do some amazing work. Many people would be drawn to these custom third party solutions which would waste the storage solutions built into the FFG boxes. Also, this can help stimulate a 3rd party economy that also ends up advertising for your game.
5) Many people use binders. I mean MANY. Some people might prefer a different box. Some people might damage their box and therefore need a new box but not be willing to buy another copy of the set. Most, people just have differing opinions about how they want to store their cards, therefore that's a lot more wasted cardboard.
If FFG had the resources, it might be cool if they designed and sold storage solutions that you could buy separately, but due to the reasons above, I don't think it's a great move for FFG to build storage into their core/deluxe/saga boxes.