I'm not sure what you're talking about. Do you mean the cost of extra DNA to duplicate? How much is it?
And your 'exact match' has deteriorated to 'exactly consistent' before you presented your first reference. The most supportive articles I know of in the scientific literature only claim to be 'broadly consistent' w/ the phylogenetic 'tree'.
As you correctly pointed out, "exact match" is inappropriate unless all the animals in question have had the relevant parts of their genomes sequenced; until then all you can say is that the sequence tree is a subtree of the phylogenetic tree.
The only exceptions I'm aware of is when the stretch of DNA with the genetic marker is deleted entirely. This is rare, and AFAIK, can be detected independently of the ERV.
Do you know what you are talking about?
I'm not a professional biologist, so I'm sure I'm missing a lot of the details, but I have read a lot about this stuff - it's quite fascinating.
No, in order for a new gene or set of genes to move to fixation, all members of the population that do *not* carry it and their offspring must be lost and replaced by new population members that carry it. No small feat. And the more differences, the higher the cost. Eventually, you just can't get here from there.
The only reason it is 'fascinating' is because you get to use your imagination to 'imagine' what may have happened.
But ultimately that's all it really is, 'imagining' unobserved 'events' that never really happened.