I know that ZC handles secrets by going from combo to combo, upper left to lower right, and replacing flagged combos with their secret combos.
I do NOT, however, know how the Trigger->SelfOnly flag works.
I'm brainstorming a trick to have multiple independent permanent secrets on the same screen by setting the secret screen state of layers affiliated with the screen (I'm doing this as a global script, fyi, so no "Place FFC here" instructions please!). I don't have any code yet, but here is my current plan:
EDIT: Sleep is helpful! I figured out how to get it down to two loops, and I'll explain below the spoiler
Spoiler: show
EDIT: Actually, if I move the check for secrets inside of the for-loop, I can get it down to two loop-throughs instead of 12 (Because the combos that have secrets would not be set to 0 on their flag, and thus would only require triggering secrets once). My new concern regards inherent flags: if I set the inherent flag of a combo, will it change all instances of that combo (X_X) or just the one at that point on that screen? I can avoid this problem too by not placing trigger flags in inherent slots, though that makes the screen setup more restrictive (Not for me, but perhaps for others who would want to use trigger flags inherently).
Oh, and one more thing. If placing the "This is secret X" flags on layer 3, I gain a multitude of extra flags to use for the script since 3 does not have ground functionality (For instance, I could use any number of the push flags to identify secrets).
If anybody has any answers to my dilemma, or if anybody has questions about what I'm trying to achieve, thank you in advance for your replies! Once I figure this out, I'll move on to expanding it for lock blocks.