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Hello Sean,

Thank you for your message.

Instead it seems as if it's entirely decentralized where each PC has a unique address, unique password/code, and unique 2FA.

Yes, Remote Utilities is a standalone software. Please note that Remote Utilities does not store any connection-related information, including remote access credentials in the accounts on our website as these accounts are needed for the support (Community Forum and the Ticket System) purpose only.

Additionally, there doesn't seem to be a way to save your configuration or profile so I can login from my Phone or PC to the same set of several PC's.

You can share the same address book across several PCs. However, unfortunately, the mobile Viewer does not support a full-fledged address book yet, so you can only add the connections to the mobile Viewer manually.
Here's a guide on how you can share your address book across Viewers.

Finally, is there really no way to safe the 2FA one time password so that I don't have to re-enter it every single time I connect?

Please note that the 2FA feature utilizes OTP (or One Time Password) which cannot be saved as the authenticator app generates new OTP every time. However, you can save the access credentials for other authentication methods, for example, the Single password.

Here's also a Quick Start Guide that might provide some helpful information, help you to set up your Remote Utilities installation and connect to a remote Host machine.

Hope that helps.