yay in the example was used to install an AUR; not to update the system which is what you are talking about. And the discouragement you speak of -Sy applies only to pacman upgrades, not AUR helpers. The only reason the y is discouraged in the wiki when installing a package is because it fetches updated data from the repos which might lag the rest of the system (and potentially the resulting dependencies if any). Most of the time it is not a concern as most (quality) software is made to be backwards compatible anyway.