Is there a way to merge windows of the same application without a "Merge All Windows" menu item? Some macOS applications (e.g. Finder or Terminal, but also third-party apps like SourceTree) have a Windows > Merge All Windows menu item that allows to merge all application windows into a single, tabbed application window.

If an application does not provide this menu item, is there a way to merge this application's windows into a single one? One example is the Atom text editor - I'd love to be able to merge the various editor windows into a single one from time to time, e.g. when just working on the laptop without an external monitor connected.

This is on macOS Sierra.
It's up to the developer to support this functionality. Many apps (document based etc. written using native Cocoa classes) support this by default. 
There's not much you can do to enable this in apps which do not implement it.