I looking to backup the Nextcloud installation. And it IS a PHP based 'website'.
Nextcloud, and I assume owncloud, do not have an automated backup option.
The backup process consists of copying data folder and dumping the database, like with any other LAMP web apps.
I'm thinking Akeeba could automate this and send it to S3.
Nextcloud backup docs
FWIW, it is possible to use remote storage, with encrypting option, with Nextcloud. But I would still want to backup the installation since Nextcloud also hosts a number of other webapps: contacts, calendar, RSS reader, etc.
I'll give it a shot. It if works, I'll post a review here.