Hmm, why would writability of /Application have any effect though?
The installation process run via Homebrew by a non-admin user[1], in a nutshell, uses a shell script that downloads app's archive, unpacks it and then uses sudo[2] to move it to /Applications. As a result, I end up with a brew:brew owned app in the /Applications directory with the quarantine attribute assigned and set.
When I run the app via my main admin user account and agree to the dialog (which is shown exactly once, on the first run only) I expect the quarantine attribute to get cleared for my main admin user. The login item is added to the gui/ domain so I expect launchd to consult the appropriate database when checking whether the login item is allowed to run.
The way I understand gatekeeper process (root daemons) and quarantine attribute (values are per-user[3]), neither writability of /Applications nor /Applications/Maccy.app should have any effect.
[1]:
$ sudo -u brew id
uid=801(brew) gid=801(brew) groups=801(brew),101(access_bpf),12(everyone),20(staff),61(localaccounts),701(com.apple.sharepoint.group.1),100(_lpoperator)
[2]: On my machine, sudoers is set up such that plain sudo uses my main admin user account and not root via the runas_default and runaspw settings.
[3]: If you run the app and agree to the warning then quit it and chown it someone else, it will display the warning again on the next run. So I'm not sure whether the actual quarantine value is preserved per file owner, per process owner or a combination of both.