I cannot seem to remotely authenticate via a PowerShell script for a SharePoint 2013 on premise installation that is using ADFS and Windows auth for authentication. In my case, all Windows Users have a deny access policy on the web application level. Is there a way to specify to login via ADFS instead of Windows auth?
Yes, there are a few solutions, but the PnP-Sites-Core solution from Microsoft outlines exactly how to do this.
The solution is a bit long to post here, so I'll simply leave it as a link. You can find more solutions if you do a cursory search for 'CSOM +SAML'.