You make excellent points, Jay. You seem to know your way around this kind of work - that is a lot of insight.
I 'see' the puckering effect you speak of - the skin is not well formed to the original contour IMO, but is adapted as best could have been done in the circumstance. I think you pegged all that well - and it is likely closer to case #3 as you cite than #1 (hydro-formed) or #2 (wheel formed).
I also will speculate that what we see in 2-2-V-1, if associated with this 'patch', is "not inconsistent" with all of that; it bears evidence of later rough treatment as well, of course, whereby some of what we see in the picture - IF associated, is probably mostly supervened by 'beach rash'. To that I will add the further speculation that the 'explosive force' we see evidence of may actually be partly or in full the effects of a human foot or similar bludgeoning effect by deliberate action to knock the panel loose (YMMV, as may other's, of course). I'll put it this way - had a human islander hungry for scraps to work with come across an airplance carcass in shallows or within reach and seen this panel - maybe partly tattered already, it may have been easy enough to get inside and beat and whack it loose. Just speculative thoughts.
Once more, 2-2-V-1 is a very odd piece of metal with some deep history in it, whatever it is. Despite many inputs raising worthy challenges (and I readily embrace the risk they may yet be true), 2-2-V-1 still has much to tell us - IF it can be discerned. I believe your thinking helps us down that path - something to look at as we study the artifact and the pictures, etc.
I'm thinking now of how it was just explained that Earhart muffed the landing at Miami to the point of having the ship examined for damage. One now wonders if some scare erupted over that and whether earlier commentary on cutting a fairly large area of stressed skins out might have been had regarding effects on strength, etc. Maybe that was part of putting a cover on with some expedited bracing just to add some stability back into a compromised area? Speculative, sure - but perhaps a test point for us.
I can't tell how the new window was braced inside to offset the removal of that much skin, but it must have been fairly substantial. I'd like to think there was no question of strength - but maybe it was ill-advised and the truth showed after that landing. Hard to say - but something to think about.