How can I stop Pipvid from managing all VLC and QuickTime windows?
You can change a setting to prevent Pipvid from snapping all windows.
Pipvid controls both QuickTime and VLC and through various methods. Primarily it uses the Accessibility features of macOS. The app specifically asks you to grant permission to do so after the app first launches.
Besides that there are a few Apple Events that Pipvid utilizes to go through menus of VLC and QuickTime, to enable Float on Top.
Finally it asks for permission to control the Dock so it can enable VLC and QuickTime to appear on all Desktops.
If at any time you want to revoke permission for any of these features. You can go into System Preferences → Security & Privacy → Privacy and then either Accessibility or Automation to revoke any of the granted privileges.