If I understand your situation, the answer is Yes. If you deploy the agent through the console, you will have to create an Automation Principle (can be a common service account) for your Remote Host Authentication, which uses PsExec or SSH to do the deploy, and that service account to do the installation. When you create your Agent Bundle, you can specify how you want the exports or users.local files to be created, and point to whatever the local administrator account name is. The local admin password will be irrelevant for that.
I know the use of Automation Principles is not usable if Repeaters and Advanced Repeaters are in use. Does this effect our ability to install the agents using APs?
no, because repeaters are not used for the agent installer jobs...