So rather than disable the system tray, or use other applications that don't have inconsistent scaled and styled icons, you'd prefer that nobody who uses Gnome is able to have a system tray?

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.

That sounds like an issue that could be solved by forcing icons and sizes for the tray.

Just give users the ability to pin the icons they care about and hide the others in a pop-out panel like Windows does.

That too, very basic feature that should be in every DE.