They do, except for the crystalline stalks.
My understanding with the stalks is that because they shatter, they will often have unique 'counters' on them (including maybe spawn time, number of times interacted with).
Probably you got unlucky trying stalks first and imagined all of them do not. Blossoms, flameleaves, roots, and bulbs all stack.
The trick is that the foraged items from different instances of the Confluence do not stack with herbs of the same type from another location. Considering the Adv Guild does not distinguish among them, I'm hoping this is more of a bug or something that could be fixed.
I don't mind the flavor with stalks and the fact that they cannot be stacked (even if personally it would be more convenient).
Here's one of the containers in my shop...please ignore the snake fangs:
In a warped treasure chest...
an elementally tranquil core: 15000 (1)
an elementally churning core: 15000 (2)
a spiky luminescent blossom: 5000 (2)
a glistening engorged bulb: 5000 (7)
an elementally balanced core: 10000 (1)
a bundle of snake fangs: 15000 (1)
a dense earthen root: 5000 (12)
a gleaming multicolored soulstone: 100000 (5)
a razor-edged oily flameleaf: 5000 (9)
