It looks like a crack to me, you can use heat to make sure. I've used heat guns, hair dryers, propane torches to help identify cracks in cast iron, apply heat and watch closely to see if it moves, grows or change how it looks
Way better to find out now before reassembling it
BTW, if it was sticking above the cylinder wall, what would cause that It should have flatten out with the honing unless you use a dingle berry hone