Does CubeBackup support multiple G Suite Domains?

Yes, this is a basic feature of CubeBackup.

Multiple GSuite domains support

CubeBackup supports management for multiple primary domains, which is especially useful for G Suite Partners, who are often responsible for managing multiple G Suite domains for their clients.

Even more, CubeBackup automatically supports secondary domains and alias domains as well.

After setting up the first domain, you can easily add more domains by following these instructions: Add another G Suite domain

Separate configurations for separate domains

CubeBackup also allows administrators to configure completely separate backup settings for separate G Suite domains.