You hit the nail. This happens indeed because you run Wayland. The only windows that are listed by wmctrl -l
are those that run on Xorg through Xwayland.
Wayland has caused fragmentation. Methods to manipulate windows now depend on the wayland compositor, so differ between Gnome Shell, KDE desktop and Sway window manager, for example.
dbus calls in Gnome Shell to manipulate windows have now been made private to Gnome Shell only. However, Gnome Shell extensions can expose dbus functionality so it can be accessed through a script.
Such an extension is Window Calls by domandoman. It allows to list windows and manipulate them (resizing, moving, mazimizing, minimizing, activating, closing). Another extension, Window Calls Extended by hseliger expands on this extension by allowing to obtain information on the currently focused window.
This is in my opinion not the ideal world: we depend on extensions. A Gnome Shell extension may become unmaintained and break in future versions of Gnome Shell.
So it will be a matter of starting again from scratch: the old ways do not work on Wayland. Alternatively, you still can decide not to use Wayland and switch to an Xorg session. This is still fully supported.