If you change relative position (or size) of a structure, it updates only if you press Done, Load or Save.
But if you rotate the structure or mirror it, you see the selection box rotation immediately, without exiting the GUI.

Old description:
If you press 'Load' on a structure block to place the boundary, then make a change, such as relative y paste value, then press 'Load', it places it into the world instead of placing the new boundary first.