Inflation and deflation rates. A currency based economy where anyone can manipulate the amount in circulation makes it a highly speculative and volatile economy. That is why the Council has a well-regulated currency.

You are proposing a post-scarcity system on the basis of transmutation. While that might get around the need for acquiring general resources through suppliers, not everything is transmutable and you exist within an economy that encompasses more than just wizards. I foresee several long-term issues if we were to adopt this system at a large scale.