Those markings would still be visible because they are below the surface and wouldn’t normally be completely removed with lapping unless you really went at it.... or it had been lapped numerous times in it’s life. Also the depth of the markings would have depended on the mood of the employee.
Looking at the top of the liner, it certainly doesn’t look like it was making anywhere near sufficient contact with the head as well as the liner not having much if any interference fit in the muff. It’s possible the liner was replaced in the past and wasn’t pressed home all the way after cooling and worked it way down after some miles. Both of these things combined would allow the liner to move around. That oil hole is more than likely too high up anyway. One way to deal with that would be to drop the liner, clean things up and reinstall the liner with the hole to the front and then drill a new hole in the correct spot. Not recommending you do that, because your cylinder muff is likely knackered. Greg is correct.... buy a new cylinder assembly and use that one for a door stop. I’m not sure if the cylinders from VOC Spares come with the oil hole already drilled so you may have to do that yourself... assuming you want to bother with it. If not you can just block off the oil feed to the cylinders.
I suppose one could put .003” or so worth of plating on the liner, but that seems a little nuts given the supply of new cylinders.