How to protect root user from root privileged custom user?

I have created a user named as <username> in my local network server and prevented all root access and password login to the server instead i use SSH authentication. I would like to know how to protect root user by validation with password if access a file belongs to root. Lets say an example,

I have updated OS by `sudo apt-get update` and first time it asks for the password. Image - Asking for the password for the first time. Image - https://i.stack.imgur.com/BH36C.png

Second time i ran any command (e.g. `sudo ls -la /root`) in which the files or permissions all belongs to root user / other root privileged user rather than me. But this time, the command runs without asking for password because session of terminal was not closed. Image - https://i.stack.imgur.com/OQAUZ.png

My concern is how can i validate all actions (terminal commands) by a user with a password if permissions belongs to root user?.

Example validation message "Those files belongs to root user, are you sure wish to continue the operation?". Image - https://i.stack.imgur.com/306hV.jpg