Yeah, I've also been disappointed when I found out that Cryptomator is really not designed to be used via cli. Still great and I use it a lot.
For your use case, rclone encrypted remotes are probably the most sensible option.
There's also gocryptfs as a faster and purely cli focused alternative to Cryptomator. It can be installed on macs via homebrew and similar solutions. Cryfs is another option.
Wait. Are you trying to say that raid is not a backup?