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Getting many alternate ads only means you are having bigger problems:
1) Topic with no advertisers
2) Pages without enough content
And the implications of lost money is not only in monetizing on those alternate ads, the lost money is also in the large member of impressions that add up in your statistics, lowering your eCPM and God knows how it screws your smartpricing and eventually your earnings!
My advice to you is:
1) Make channels your friend and IDENTIFY exactly which pages generate the most alternate ads.
2) Either fix the content to show ads or exterminate Google ads from there as soon as you can.
3) Now you can easily monetize those pages through another network.
While on topic, I get down on my knees and say:
a) Please allow us to use referrals as alternate ads to keep the money in the family ;-)
b) Please stop counting ads you did not display (alternate ads) in the ad impressions, it does not make sense!
The hardest part is that you can't see the ad to check it looks ok...
for this just build a simple html page and put an iframe on it that matches the size of your alternative adblock.
point the iframe to the page of your alternate ad.
make the rest of the page grey or something.
Load this page in your browser...you don't even need to put it on your server and you can see what your alt ads look like.