Let me start by saying this is internet advice and a proper contact inside the enterprise with knowledge of the particular implementation and knowledge of the internal procedures and security policies needs to be involved. The ISSO/ IT Security Officer is the only one that can really provide an answer.
Now, based on my personal opinion, it really depends on your enterprise policies and the flow you are trying to cover with rclone and how it's implemented.
On top of my mind, proper file permissions for rclone.conf, log retention for file transfer validation, disaster recovery access etc. would be the bare minimum.
I would steer away from anything that can be accomplished by a tool included by the OS like ftp, sftp, scp, etc. Just use that one and avoid the questions on why you went with another tool.
Whatever architect is working on the implementation would need to involve the security liaison involved to get approval of using the application. Any vulnerability scanning would also need to be monitored, patch accordingly and assess if the vulnerability impacts your implementation and use case.
I would doubt you can get approval for crypt as enterprises usually prefer using off the shelf encryption solutions to minimize liability.
While I'm confident rclone would have no issues passing a general audit, I would not even think on using it for anything that might be considered PCI or SOX relevant as the external auditors can start asking too much documentation that might not exist.
But for a basic security audit, just proper permission to limit use of the binary and configuration file to the required UID and other security measures, proper documentation for change management on any release update or configuration should be enough.
Please note this would only cover the use of rclone, from a security audit it would also need to cover the remote you are using, how is that access controlled, password management, auditing of access of the data outside of rclone, etc. Which might be more work than actually the use of the application.