What I don't understand is how courts can assume it's used in a crime before a crime has been proven in court.
Presumably, if I can prove I earned/bought something, and am not convicted of a crime, turf the government seizure is wrongful and I should get restitution, but from what I read, that doesn't work?
Only persons have the presumption of not being guilty. Not property. The government can claim crimes all they want, they just can't claim a person committed a crime (and punish them for it).
This is all about shifting the burden of proof to the accused. Allowing the money to be charged separately does that, or so courts have ruled.