the 'mitochondria eve' is merely the date approximation of the woman whose mitochondria genes have replaced all the other variations from her time period. Other genes will have a different time frame in which a specific strain became dominate. The 'Y' chromosome dates back to the man who is the great great great (unknown number of greats) of all the men of hte world.
Let's look at it this way. YOu have 5 woman. Each woman has 3 kids. One woman has nothing but boys. Her mitochondria dna no longer is in the gene pool, yet her genes are. One woman has 1 girl, and two boys, and her girl has nothing but boys. .. her mitochondria DNA is elminate from the gene pool. Repeat for a long enough time.. and sooner or later, just one of those 5 woman will have their mitochondria DNA prominent over the rest of them.