Here's a modification on your idea Rem, what if each player is able to build just 1 "alchemy tower" or whatever structure, now by itself this structure would produce no income, but it has an inventory with several slots, and if you place a special item such as a crystal in a slot the structure will slowly regenerate some funds, the more of such items are placed inside the building up until the slots are are all filled the greater the income generated by the "alchemy tower".
Edit:
In order to avoid abuse such as carrying over the item from one map to another via a hero's inventory the item should be "absorbed" (like ruins) once taken by a hero and automatically given to the "alchemy structure" if it exists or should be given to it once one is constructed, I just thought about this while having a discussion on the subject.
There are lots of other ways to do this, I can propose a bunch of ideas but I think this is the better working one, and with the properly implemented safeguards it can't be abused like other ideas.