>If the police confiscated everything you owned to cover a fine for $100, isn't it reasonable to get the difference back?

Legally this is correct and exactly what happened.

The reason this is becoming an issue is that all the bitcoins that were seized were from selling drugs. The point of the fine is to match the profit of the crime so reasonably it should have taken all of the bitcoin regardless of the underlying value.

If he had sold drugs for a gold ring and then the price of gold went up, should he have gotten a bit of the ring back?