This is how Equake originally worked, but it is simpler (and slightly faster) just to hide the frame on “close” and then unhide it on “re-open”, and this became the default behaviour for Equake some time ago. Essentially, opening a new window under GNOME Shell Wayland can result in that window being placed on top of any existing windows (though to do it properly, employing a it of Elisp (select-frame-set-input-focus (selected-frame)) seems to result in the new Emacs client frame being on top (and focussed) [this is a potentially useful trick for opening regular new Emacsclient frames as well].