borgmatic dev here. What I do is run borgmatic locally on each server that needs to get backed up. That's a whole lot easier IMO than setting up network filesystems / rclone or tunnels or screwing around with database dumps yourself, and potentially more reliable. So in your case, I'd run borgmatic on the VPS and then have it connect locally to your MariaDB database using borgmatic's native filesystem support. And then if you also backup the local files with that same VPS instance of borgmatic as well, there's nothing to "merge."

I'd generally recommend one Borg repository per source server / instance of borgmatic.

Lastly, my raspberry uses rclone to push to S3 and I don’t want the keys to be accessible on the VPS’s, that’s why I’m trying to have borgmatic only on my raspberry.

You could always have borgmatic backup to a local Borg repository on the VPS, and then run rclone on your trusted server to copy that repository to S3. Personally I'd probably just put the S3 keys on the VPS and lock it down so that I trust its security, but you do you. 😀