I'm certainly not Geoff, but I will try my best to answer with my interpretation. In Phase 2, with the days/workouts switched, the focus gets placed on the grinds, which is more effective for in producing the desired goals. At the end, if you've noticed, the testing is for the grinds only, not the ballistics.
The rests between A1 and A2 do not change. A1, rest, A2, rest...so on and so on. The only change is that you are more fresh and recovered for those days and should be able to do more work to reach the desired goals.
Hope that makes sense.