For me the difference between the two commands is the following:
Activate Reference will switch to that Viewpoint which is currently the source of the Trace Reference. The Reference setting will be the same IF it applies and makes sense. So for example, if it is set to show the Floor Above, then it will now show the Floor Above the activated Viewpoint.
For example: Ground Floor is active and Floor Above (First Floor) is set to be the Trace Reference. If you activate the Reference, then now First Floor will be the active, and Second Floor will be shown as Trace Reference in it.
If the current Reference Setting has no meaning in the Activated Viewpoint then it will show now Reference.
For example: The South Elevation is shown as Trace Reference under the Ground Floor Plan. If you use the Activate Reference command, the program will switch to the South Elevation Viewpoint and no Reference will be shown.
Switch Reference with Active will switch to that Viewpoint which is currently the source of the Trace Reference
AND will show the currently active Viewpoint as a Trace Reference in that Viewpoint. So basically the roles of Active Viewpoint and Reference Viewpoint are swapped.
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