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Dear TK,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
Per the description shared, I would like to summarize your concern i.e., when you check the permissions for any member or the owner of the site, you see the "Deny - Add and Customize pages" even for the user with the Full Control permission.
If my understanding is correct, I would like to you know that the possible reason is custom script is not enabled on the SharePoint Online site. So, I suggest you turn on the Custom Script at the both tenant level and site level to check the result.
Reference: Allow or prevent custom script - SharePoint in Microsoft 365 | Microsoft Learn
Thanks for your cooperation.
Sincerely,
Mia | Microsoft Community Moderator