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.