I recommend you mark the top of the piston in relation to the discoloration in the cylinder. You may need a piston due to a casting defect or possibly a wrist pin has rubbed the cylinder wall.
If the top ring is seized in its groove, there is some kind of physical damage that has been caused in the past by a solid item inserted through the spark plug hole to check piston height. (I've seen a person ruin an engine doing this).
Keep in mind that the are mass produced consumer engines, so machining tolerances are not strictly checked on every engine.