If I buy a Humble Bundle not beating the average, can I later pay more to beat it and get the extra games?

Yes, you can do that. Go to the specific page of your humble bundle, not your account. There you will see a link to increase your purchase.

Clicking this link will open the payment options:

As you can see, it already "knows" how much you paid and you can top it up to any amount you wish or need to beat the average and after paying you will find the new keys below on the same page.

I can verify that after the sale goes away you can add up to the average and still receive the codes for the extra games.