The question asked: "Steve, should we leave our coordinate system icons clipped or un-clipped?"
My Answer: As we know, the Project Base Point (PBP) and Survey Point (SP) can be un-clipped. If they are untouched we'll find them clipped.
When these are clipped the symbols for each of these are attached to the coordinate systems they belong to. That means moving either while clipped will alter the coordinate system. If this is done unintentionally, or by someone who does not realize they have been adjusted intentionally already, the coordinate system(s) will be changed.
Therefore I'd say it is not unreasonable to leave these in their NOT clipped or un-clipped state at all times, especially after they have been adjusted intentionally to align models or survey data. If they are not clipped then accidental movement of these icons do not alter their related coordinate systems. It merely changes the symbol's position relative to their coordinate systems.
I regard these symbols as markers or annotation when they are not clipped. In this state they are harmless to our coordinate machinations. Clipped they pose a danger to our careful adjustments to align models and site information.
My opinion: Keep them Not clipped, un-clipped.