I got this to work by cheating a bit. It seems that the limitation is only for autonomous programs so I thought: What if instead of setting my program as autonomous, I set it as a skill? It turns out it works and it seems that there are no limitations due to it runing as a skill. Right now I am able to detect a hit (still only gel beads though), turn to the side of the hit, zero in into another S1 and fire! It always use whatever is the mode selected (gel beads or IR).
That is progress at least.

An excellent "hack"!  That is progress!  I'm telling all the new S1 owners!

The other advantage of launching the program as a Custom Skill is that you can launch it remotely.

Hello and good day BGA. Thank you for sharing this information here at DJI Forum. This information is very helpful. Great work and thank you for your valued support.