I prefer not having to worry about it at all, and I don't. Its tidy by default and stays tidy no matter what I install. Many other "deficiencies" in Gnome, like the lack of desktop filing, or the austere file manager contribute to this tidiness.

The first versions of Gnome 3 did indeed have a system tray for backwards compatibility, and it was hidden out of the way until you needed it. Eventually it was scrapped once enough software was updated to not rely on it.

If somebody insists on having a messy UI, they can use literally any other DE available for Linux.