Yeah, and the prefab system uses the copy/paste system internally so they should behave the same...
The only thing I can think of that could differ is how editor_arrayify_patternobject subtracts the editormarker's position from each point in the path when copying (to get relative distances that can be rotated), does that somehow act differently when loading a prefab because the marker could be anywhere perhaps? (instead of a place that includes the path's origin, which is guaranteed when copypasting)