I would not be worried about your machine shop as much internet know it alls the marks in your cylinder are not a problem a bore gauge is the best way of knowing if the bore is ok not an eyecrometer the marks are due to distortion and uneven wear but probably won't matter if a ball stone hone was used u wouldn't see it but the low spot would be there with out measurements like out of round and taper you can't make that call from a picture. IMO boring it over the small amount that an oversize piston is will have little or no effect on strength.
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