Not sure whether it's a bug or not. When the target app of org.kde.plasma.appmenu has no menu, the applet is hidden and neighbour applets are shifted as a result since the height of appmenu is zero when this applet is hidden.
That's just how applets work. Same as Task Manager or system tray: content size may vary and it's absolutely normal. Not sure what could possibly be done about it, to be honest.
Yeah, seems you're right.