Is there a way to add the Company Administrator as the primary site collection administrator for all site collections using PowerShell?
You can use the PnP PowerShell commandlets to do so. A nice example of what you want to achieve can be found at:
More information about these commandlets can be found at:
I tried the set-sposite command but it requires an actual email id for owner tag, I cannot put "Company Administrator" in there as the user doesnt exist.