Can I claim California's final paycheck penalty if the unpaid amount itself was small?

Yes, and this is actually where the statute does some of its most meaningful work for workers. The penalty calculation is based entirely on your daily wage rate, not on how large or small the amount that was actually withheld happened to be.

As a concrete illustration, someone earning $200 a day who was shorted a single $180 final shift could still generate a penalty worth several times that original unpaid amount, since the penalty accrues daily at the full daily wage regardless of how modest the underlying shortfall was. This is one of the relatively few situations where pursuing what looks like a small wage claim is genuinely worth the effort.