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How can mutations in mitochondrial DNA be used to trace…

How can mutations in mitochondrial DNA be used to trace ancestry if there are hundreds of mtDNA molecules in a cell?

I've been reading about mitochondrial DNA and the mitochondrial Eve and now I got very confused. I have a background in molecular biology, so I'm familiar with terms, but the concept of using mutations in mtDNA still confuses me. When we say that two populations differ in mutation at a certain position, does that mean that all mitochondria in that cell/individual have that mutation? Because if I'm not mistaken, each mitochondrion has several (up to a dozen) mtDNA molecules, and there are hundreds of mitochondria in an egg cell. Shouldn't out of those hundreds or thousands molecules different mutations be dispersed across mitochondria? Since I assume those mutations are silent point mutations (no effect on phenotype or organel/cell survival, shouldn't all of us have a big mixture of various mutations? How can we then make a consensus sequence to compare? Especially considering we are testing somatic cells which could have extra mutations from that generation? Am I just overinflating the rate of mutation in mtDNA?
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