Ruler trumps chain checker.
Use the checker for a quick check. You now know that it reads .25% high on the .75% scale.
Not uncommon at all for them to be "generous".

You might want to use a 3' section of tape measure. It'll give you 3X the resolution vs checking a 12" section. I use the 1 & 37" marks to avoid dealing with the hook.
That would give a little better idea of the chain checkers true error.