The tree is unlocked after the temple sequence and you are in the live world. So you don’t have to complete the tree in a linear way.
The reason they aren’t physical assets is because you only need them once, which made them a single craft item which you only did once then never need to craft them again. They don’t break, wear or disappear and adding a reason for them to vanish felt a little forced. Plus it takes up an extra inventory slot and we would need a Ui screen for you to customise, slot items in and so forth.