NW3,
Your scenario could happen....however, bear in mind that you're through 2.4 going to 6, and the GA is at 150ft(ish) just starting to go to 3. If it looks tight, we'll stop the GA at 2. It's just belt and braces...usually there's enough lateral separation to allow the GA to continue to 3....by which time you'll also be through 4, if not reaching 6!
The whole point of the exercise is to verify your Mode C. If the scenario you mention did happen, and we hadn't got a level check, then we wouldn't have the option of using vertical separation. Doing so just keeps our options open.