Most things that Provisioning (or generally, our agent) does will run as "Local System", correct.
If you need to run things in a specific user context, you will want to make it a "proper" distribution package & set the user you want to run it as
... if this is before joining a domain, use ".\{LocalUser}" to ensure you're authenticating / running as a local user. So for instance ".\administrator" if need be.
Alternatively you can use a "RunAs" command-line tool that comes on Windows:
- Runas - Run under a different user account - Windows CMD - SS64.com
... but that does tend to require an interactive password filling out thing.
But there's this on technet too -- Script Automate RunAs Password Entry -- so ... "pick your poison" (I'm offering up various options as having choice is always a good thing, and sometimes you NEED to run things offline or whatnot).