Everything you’ve encountered is already thoroughly explained in GenP Guides, including the Troubleshoot Section and GenP Setup, Troubleshooting, and Best Practices Guide.
The UPX Error Code 2 simply indicates that the target file was already unpacked, so there was nothing further to unpack.
The Accept Terms popup you’re seeing is non-AGS-related, it is treated the same way as the Unlicensed popup.
Premiere Pro: Patch normally, then run WinTrust if non-AGS-related popups (like Accept Terms or Unlicensed) still appear.
If you prefer not to use WinTrust, or experience issues after using it, untrust the app and use the modified config.ini instead to allow unpacking and patching.
After Effects: Patch normally, however as clearly stated in the guides, WinTrust should not be run on it, use the modified config.ini instead to allow unpacking and patching.
If those do not resolve the popups, you’ll need to fallback to alternative methods, such as: using modified hosts file with any additional domains found, temporary workaround method, or firewall rules.
Keep in mind that modified hosts may not work for every user, and you may not find new domains.
If that happens, use the temporary workaround method or firewall blocking as a last resort.
All of these approaches are described in full detail in their respective sections of the guides, review them carefully before proceeding.