Hey, Simon

Always fun playing with you, man, want to clarify this issue for you.
Alchemist takes gold twice, and that's not a bug. First time he takes gold as a compensation for the building confiscated by the magistrate (look at it, as if it's government money he gets) the other money he gets for his skill (look at it as money from his god) so, those money come from two different sources.
And that looks like a bug, first I was confused too. But, in fact it's fair, cause when magistrate confiscated other characters building, the balance is restored and both get equally.
When alchemist builds a building - it's his advantage. He's left with extra gold.
So, it fair in all ways.
Have fun, buddy, hope to play with you again!