It's from Latin in- (meaning "in" or "on") and dorsum (meaning "back"). Indorse comes to English through medieval Latin, and changed forms in the 15th century to endorse, around the time the roots of our modern court system took roots in Florence during the Inquisition.

The Florentine republic relied heavily on maritime trade, and so the court system was generally modeled around adjudication of Maritime law. Using the older Latin form lets creditors and courts know that the Sovereign is asserting Commerce law, the Law of the Land.

Am I making this up? Maybe.