Cylinder wall problems ( never seen anything like it)

It looks to me like the ring seal is gone. Way too much carbon below the top ring. I've seen bores stained like that - it was water that did it. The walls might feel smooth but in reality the honing process tears the metal on a microscopic level. Rust can form below the level that the rings ride on. It can form from condensation - when you run E-85 or methanol it holds water - gasoline does not. I wouldn't sweat the marks. The ridge tells me the 2nd ring is messed up which might also be a part of the sealing problem.