Yes they need to be placed somewhere, they are not stored in the dgnlib.
Taken from ORD help files:
Spot or Spot Elevation
Points (with X,Y,Z data) that have no functional relationship to any other point. Random survey shots in open terrain would be an example of random spots. Point elements…
In the Explorer, you can remove it or modify the properties.
The graphic manipulators are not showing up when civil elements are selected.
Aha! I see that I do not have a "Drawing" folder for Plan. Maybe that explains it?
Yes, it would be great if these issues didn't occur with updates to Windows. Unfortunately they do exist because the OS can change supporting files which our programs are developed with and we cannot foresee these type changes. We just have to try…