Hello Haris Brkanic,
Thank you for posting in Q&A forum.
Based on the description "In "Domain B" GPO with "loopback processing configured" (GPO#1) is applied to "Computers_B" OU as well as GPO with needed user's settings (GPO#2)", I understand Computers_B OU has computer objects in domain B, you configure loopback processing ("Merge" or "Replace") (GPO#1) and link (GPO#1) to Computers_B OU, and you configure some needed user's settings (GPO#2) and link (GPO#2) to Computers_B OU.
Now as a test, you signed one domain user (such as U1) from "Domain B" (different OU as Computer B) on one machine in Computer_B OU (such as PC1), you can check this domain B user settings as below:
1.Logon PC1 using domain B user account U1 (that applies this gpo).
2.Create a folder named F1 in C drive.
3.Open CMD (do not run as Administrator).
4.Type gpresult /h C:\F1\gpo.html and click Enter.
5.Open gpo.html and check if there are needed user's settings (GPO#2) under "User Details" if it is "Replace" mode.
Or
Open gpo.html and check if there are needed user's settings (GPO#2) and U1 user settings under "User Details" if it is "Merge" mode.
https://learn.microsoft.com/en-us/troubleshoot/windows-server/group-policy/loopback-processing-of-group-policy
I hope the information above is helpful.
If you have any questions or concerns, please feel free to let us know.
Best Regards,
Daisy Zhou
============================================
If the Answer is helpful, please click "Accept Answer" and upvote it.