You can't enable/disable ClickOnce for only some sites in Edge. If you set ClickOnce Enabled, it will enable for all sites. If you set ClickOnce Disabled, it will disable for all sites. AutoOpenAllowedForUrls has nothing to do with ClickOnce setting.
For your demands, I suggest that you can provide feedback to Edge team by pressing Alt+Shift+I in Edge. They will check the feedbacks and improve the product continuously. Thanks for your understanding.
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Regards,
Yu Zhou