Hm, does seem like the materials and crafting is story locked.

Item progression is fairly well gated as the story progresses. A few tips:
- Take advantage of multi output recipes to stack up trait levels. A max level +atk/def/spd can do a lot of work. Zettel and water orb are very good at trait stacking because it just keeps going back into more and more items.
- High quality ingredients can feed back into recipes to create superior quality ingredients. Don't go crazy on it, wait for a tech from Ryza 1 to unlock first.
- Upgrade armor and equipment early on. Weapons are a bit more effort to personalize for everyone.
- Pay attention to combat items and try to get a few strong nukes. Ryza is of course your strongest item user but other characters can work well with support items like debuffs and heals.

Have finished the game. Can say that there are some items that can be sequence breaked by giving romy stuff. As well as getting it from the old zones deluxe bonus. But there will be plenty of times where you had to progress the story to get what you need.