You're asking three different questions, only two of them are related to each other.
Your ability to block rclone on a network device depends entirely on what it accesses.
I would assume the app just calls the various APIs for AWS/Azure directly.
Which means: to block this app, you'd need to block access to these services.
However, that is just a guess and I recommend watching the various logs on the gateway to confirm what it does.
At this point, there is no monitoring mechanism for Identity Collector.
I believe this is planned, but if you have specific requirements, reach out to your local office with an RFE request.
An individual Access Role is an "and" for each of the configurable options (User Group, Machine, Network, RA Client).
You can create another access role that specifies Machine without the User Group.
However, some user must log onto the system for a machine identity to be acquired.