What different effect did you see?
The main difference is in where the package gets built, as you are the root user not your own user, the cache will be in a strange place and some config files may be misplaced.
Also, running as root is dangerous as the aur uses random scripts made by strangers on the internet. (edit: as stated by OP, mkpackape refuses to run anyway) This can be very dangerous, even when not run as root. I've seen an ip logger next to a list of "people who can fuck themselves", fork bombs, and have heard of crypto miners being installed. All in large well used repos.
Cemu, nordvpn, certain browsers, and many more are not distributed by their owners
Giving these scripts that are often made by some random person root access is asking for damage. People could just put dd if=/dev/random of=/dev/sda inside it and boom, your drive is not only gone but you can't even recover your data
Edit: they are correct, yay will simply refuse to install an aur package using sudo, apologies for suggesting otherwise