Even a brand new chain has some play in the rollers (varies with brand), so unless the chain checker is compensated for that it will show a new chain as having some wear. Also most checkers measure over a short distance so the added roller play can add significantly (in proportion) to the perceived pin wear.
This isn't to say roller play doesn't matter (it does) but the 1/2% rule of thumb (1/16" over 12") is based on pin wear only, with the roller wear imputed. Adding it then is essentially double counting.
Most people that have gone this route, use a chain checker as a screening device, then confirm with a ruler.
BTW- it is possible to properly integrate roller and pin wear, and some chain companies use their own replacement guidelines based on combined wear. However, to my knowledge, none of the gadgets sold as chain checkers are properly calibrated to factor the roller wear, and therefore read high.
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