Now please re-read the above and:
Substitute "sport" for a type of job (and "men" for "women" if you wish) - we are back in present day society where people scream discrimination because numbers aren't 50/50.
The assumption here is that 100% of the cause for every notable gender imbalance today is due to inherent differences. I think that's pretty naive. Can you name the year when equality happened? Because what I observe is consistent change from 200 years ago, which basically agrees was non-equal. On what basis do we say that today, or 10 years ago, or whatever was the time when we hit equality?
Frequently on slashdot even the suggestion that we formally study the reasons instantly triggers huge comment threads about inherent differences, bringing up red herrings like conscription or circumcision -- things that are generally agreed to be unfairly anti-male as if it disproved that there was anything unfairly anti-female. If you can flip it around and have somebody say they won't support ending conscription for men only until there is pay equity for women, it makes exactly as much sense.
When you see a persistent difference, there's two possibilities. There's an inherent difference, or there's a cultural difference (or some combination). The instantaneous assumption that all observed differences are inherent is extremely convenient. Even if true, it's worthy of testing.
So yes, a true meritocracy will end up with differences due to various natural factors*. But we haven't seen a true meritocracy so we don't know what it would actually look like.
*Actually, there's reason to fear that a true meritocracy is an unstable system, almost inevitably devolving into a less globally efficient one due to the local efficiencies of stereotyping. After all, it's not like you can rationally say that our 6 million year ago ape ancestors had an unnatural society. But there's clearly been weird cultural biases in many times and places. Any unreasonable cultural biases came about sometime.