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I agree this is a big problem. I've had cases where I'm still reviewing stuff but the person whose code was under review just fixed my first few comments and then submitted it while I was still writing the rest.

I know this is partially a process problem, but having batched emails would certainly help make it more obvious.

Google's reitveld is a bit of a mess but at least it gets this part right.

On the topic of github emails, I'd love the ability to set an email for notifications on a per repository, instead of just per organisation basis.

Can't you turn off emails but still have GitHub notifications on the website?

You can. I had to do this because my GitHub username (like my HN one) is just my name ("rob") and I was getting notifications from people using @rob in their comments/replies instead of the person's actual GitHub username. :)