In the past I have helped a user that dragged lots of files out of /Applications to their desktop, and assumed it would create a shortcut like Windows.
Their system tanked. Nothing worked.
I had to talk them though the process of getting the apps back into /Applications. It has been awhile, but I think it was done in Single User Mode with mv commands.
I have seen users move System Preferences and things break. I ended up diagnosing the problem.
I have seen users remove a an app, have an updated app put in /Applications, but because they had the app on the desktop and double clicked the old app on the desktop, they did not get the functionality advertised in the new Mac OS X release (it was awhile ago). I had to figure that one out for an irate user that insisted the new app was broken.
There are real events I have seen and helped people understand what went wrong.
I'm sure Apple Support has received lots of calls with users whining that their system is broke because they moved things around inside /Applications. Either moved apps out, or created their own subfolders and moved apps into the subfolders, etc...
Feel free to educate all the developers that they cannot go looking for an app in /Applications or /Applications/Utilities and must use other means of searching. Herding "Cats" is always fun 😀
And all installers to not assume an app should reside in /Applications, but rather search the entire disk to find where it might live (or if there are multiple copies where they live) and update the app where it is, as apposed to installing a new copy in /Applications. I'll use the "Pushing a String" analogy this time 🙃
I've been a software developer for 47 years, working on platforms that boot by toggling in the boot code on the front console switches, to booting from 80 column punched cards and punched paper tape, to booting from magtape, floppy disks, hard disks, and SSDs.
I have yet to see universal consistency between developers. Not even when they are in the same group, let along different companies.
My advice. If the app installs itself in /Applications or /Applications/Utilities or even ~/Applications, let it alone and create your own folder of aliases if you just want a frequently used subset. If the application comes in a .dmg or .zip file, you can put it anywhere you like, just try to be consistent so you do not end up with a dozen copies over the years.
You may not like my advice, but your system will have fewer problems over the years if you follow it.