Q1: Do both applications use the same physical copy or are there two copies?
They are both the same copy. Both apps analyze the location where the photo is stored and the location contains only one copy of the file. If you have 5 copies of the same file, in the same folder, both applications will show you 5 photos instead of 10.
Q2: Is there any special arrangement between Google and WhatsApp because I do not see anything about it in https://drive.google.com.
I assume yes. On Android, WhatsApp uses Drive for backups, while on iOS, it uses iCloud.
Q3: Does this mean that WhatsApp's photo B is saved to my Google Drive account, as well as the Google Drive WhatsApp special backup on the X account?
Yes. Although the accounts are different, both applications have been configured to access the same folder (in this case, WhatsApp Images). Thus, when saving files, they both save the same files in both accounts.