Yes, you can do such thing with Cryptomator but I don’t think it is here the best tool to use. You want to store your data encrypted on the other machine, so you need just some encryption service/daemon on the other system
Cryptomator is a user application and intended to encrypt your data locally and then transfer the data then to some location. It encrypts each file for its own (in contrast to veracrypt), so only changed files will be updated ind the remote location. Additionally it obfuscates the directory hierarchy.