This is all covered in the Troubleshoot Section of the GenP Guides if you read everything related to WinTrust itself.
WinTrust does not replace the hosts file; rather, it is an additional feature introduced in GenP. It is intended to be used after patching, especially in cases where unpacking and patching do not fully cover certain apps.
While it may seem like WinTrust replaces the hosts file, it's more accurate to say that it eliminates the need to rely on the hosts file or firewall rule methods. In essence, it provides a newer and more effective option that is now recommended to use before falling back to older methods like modifying the hosts file or setting up firewall rules.
That said, you're still free to use the hosts file or firewall rules if you prefer. However, with recent GenP updates, the combination of unpacking, patching, and applying WinTrust, if needed, should effectively block all non-AGS-related popups.
For AGS-related popups, like the Adobe Genuine Service popup, there's a separate, easy method provided in the guide to remove those as well.