Is that actually necessary?
I can't test this on my Pentair EasyTouch system, because it allows a maximum of only 12 schedules and I'm already maxed out. But if your Jandy system doesn't have such a low limit, it seems to me that you could set up six PAIRS of 2-minute spillovers, with the schedules in each pair separated by 30 minutes (e.g., schedules at 12:00 and 12:30, 4:00 and 4:30, etc.).
This would ensure that exactly six of the schedules would run while the system was in Pool mode, regardless of what time the Pool-mode windows happened. And the other six schedules would run while the system was in Spa mode, and so would presumably have no effect at all.