Preferences under Edit (Linux), Tools (Windows)
It looks that the preferences are not under the same menu for Linux and Windows. I have Zotero 5 installed in Windows, where the preferences are under 'Tools'. However, for my other installation of Zotero 5 in Linux the preferences are under 'Edit'. Related post https://forums.zotero.org/discussion/65794/i-cant-find-the-preferences-window-in-the-5-0-version
Gear menu aside, this isn't new, to be clear — this has always been the case in Standalone, and in Firefox since, well, since before it was Firefox. But it looks like Mozilla was basically following Microsoft's lead, and I think those Microsoft programs either no longer exist or have switched to ribbons and no longer have menu bars (let alone Tools menus) anymore, so it's probably reasonable to move this, along with renaming it to Preferences. I agree that Edit -> Preferences is more intuitive, if no one has compelling examples of Windows apps that still use Tools -> Options.
(It won't be the same on all OSes, though, because on macOS it definitely goes in the application ("Zotero") menu.)