What do you mean with “safe”? It is beta software and this means some feature can change until release or there can be bugs.
Technically the agent don’t report back to some server/instance. It is only queried by the instance. Inside the agent you can configure if it only should answer a single IP or many or all. All information about the agent can be found here Monitoring Windows - The new agent for Windows in detail and Monitoring Linux - The new agent for Linux in detail
In the normal environment there is no registration. CMK only needs an IP or an name instead of IP that is resolvable. The whole procedure of agent registration for automatic update (that is the only reason for the registration) is described here Automatic agent updates - Distribute agents and plug-ins automatically
If you do this with a script you should create an automation user with only the right to register the agent. With this user it is no problem to have a password (secret for automation users) in clear text inside your script.