I agree it looks like a scratch, but what made it that deep in the bore? i suppose a skirt could do it. Any chance you have the piston that came out of that cyl? Any debris down that low would have to come from the crankcase, right :)
Here's That Piston (Untouched, as it came out)
and the Line as seen from the top...
It's 3 1/2" down from the top So, it's Under the Rings.
I didn't do that Honing it... It had a (Very Bad) Previous Rebuild. Sorta. The Ring Gaps were All Waaay Too Big and it Smoked, Alot.