I personally do not allow this method in my company. If the net name is different it is not allowed to connect unless an "alias" (from Concept) body is placed on it or it has a secondary name (OrCAD). Either method reduces the net to one physical net in the board and the IPC netlist works.
Your method sounds like you're trying to fix something in the layout that has an elegant solution back at the schematic.
Kudos to your boss. :)