Technically, you only need the public key to encrypt data, not decrypt. Decryption is the job of the private key. Unless I'm misunderstanding your use of the term.

As far as I'm aware, rclone does not use asymmetric encryption (public/private keys), since you're not encrypting the data for anyone else, so it's not really necessary.

I suppose that any program implementing the scrypt algorithm should be able to work with files encrypted by Cryptonator.

As far as programs that are just plain encryptors, there are loads out there - 7zip, VeraCrypt, GPG, and even rclone. Out of those 4, only GPG implements public/private key cryptography, since it's intended for sending encrypted messages to other people, rather than just storing the data for yourself.