electron-menubar popover appears depends on the display server. The visual tests confirm that the tray icon and popover window render. They do not assert that the popover is positioned next to the tray icon.
Native Wayland
On native Wayland, tray-anchored positioning is not possible, and there is nothing the library can do about it. Two protocol limitations stack up: an application cannot set the position of its own window (setPosition is a no-op, getPosition reads back [0, 0]), and the tray icon, hosted by the panel via StatusNotifierItem, reports no coordinates. The compositor decides where the popover appears, which is usually the center of the screen. menubar logs a one-time warning when it detects the window could not be positioned.
X11 and XWayland
Under X11 / XWayland, an application can position its own window, so the popover is placed wheremenubar computes it. (Some Linux panels still report no tray-icon coordinates over StatusNotifierItem, in which case the window falls back to a screen corner rather than sitting exactly under the icon.)
Workaround
If a Wayland session places the popover in the wrong spot, running under XWayland with--ozone-platform=x11 restores positioning.