Nice theory bro, you have some points.
As for me, I understand it as Madara surviving his battle with Hashirama, then living in difficulty and pain thus awekening rinnegen (his own set of eyes). Summoning the Gedo Mazo, then "transplanting" his rinnegan eyes to Nagato. And the only way he could do this without Nagato knowing is through Izanagi.
Thus when he transferred his original eyes (with rinnegan), he used the spare eye to perform Izanagi which explains why in the panel one of his eyes was closed.
As for me, I understand it as Madara surviving his battle with Hashirama, then living in difficulty and pain thus awekening rinnegen (his own set of eyes). Summoning the Gedo Mazo, then "transplanting" his rinnegan eyes to Nagato. And the only way he could do this without Nagato knowing is through Izanagi.
Thus when he transferred his original eyes (with rinnegan), he used the spare eye to perform Izanagi which explains why in the panel one of his eyes was closed.