I hadn’t actually considered that before. What’s your preferred way to do that?

The creator used Apple (iOS) exclusive privacy features to run the service. They commented on it publicly a few times. Also why there was never an android version.

Why write off iCloud? Just turn on the advanced data protection feature for end to end encryption.

If you want to self host, while I’m not familiar with Goodnotes I bet you could write a simple Apple shortcut to take those files to a storage provider like nextcloud then just automate that shortcut to run daily, weekly, whatever.