The image above shows the initial position, in a Building file, of the PBP and SP after using Publish Coordinates to pass the Shared Coordinate system information from a Site file to it. You can't see a building because they are quite far apart...which is why the icons do not change size when you zoom in/out.
When we open the Building model the Survey Point (SP) is marking its own origin, which is 0,0,0. When we examine the Project Base Point (PBP) we'll find coordinate values that indicate how far away it is from the SP. If we un-clip the SP we can choose to move it closer to the building and we'll see the coordinate values change to show how far the icon is moving away from its origin .
When we use Acquire Coordinates Revit moves the SP (when it is Pinned) to mark the location of the World Coordinate System origin (WCS assuming a DWG site source). When we use Publish Coordinates on the linked Building file it does the same thing but remember the SP is marking the WCS origin, which is 0,0,0 in the DWG...and for the SP of the building model too.
I hear and read the following a lot...
I then test it by removing the linked building model and re-link using shared coordinates and it works.If you're tempted to do that, just don't do that on real projects since it opens the door to messing up the work we've just done. Just link the building model, re-position it and use Publish Coordinates. Then leave it alone; unless design changes require it to be moved again. A better test? Link the Site model into the Building model using By Shared Coordinates. That doesn't change anything you've done and you'll see they line up properly.
Placing a few spot coordinate annotations on this fine building design, after zooming in closer, looks like this. Also, the one closest to the PBP is assigned to PBP while the others are assigned to the SP.