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The rooster has nothing to do with blood spots or meat spots. That's entirely dependent on the hen's body.
There is no difference in taste, appearance (unless you look hard and know what you're looking for) or nutritional value in fertile eggs vs. unfertile eggs.
Here's some info. on blood and meat spots that should help you:
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What you are describing is chickens mating. It's not pretty. However, it does get better once the hens get to laying age. Once they submit, it happens quickly, without a fuss.
IMHO, a rooster should live with his hens. It's where he belongs, protecting them.