Yes, there was a lot there!! :P... like years of genetics so don't feel made.. you are asking good questions.......Points 3 and 4, yes. 1 and 2... I have to explain a little more. And 2, it is not what "I" believe.. um, i'll have to explain more. "Alleles" in the terms of this type of testing (the STR (short tandem repeats) are different, will its a different concept than the ABO blood groups that you are talking about, and percentages in that sense. Those are genes, that code for proteins on blood cells, obviously. The short tandem repeats are present in non coding regions of the DNA. This dos not help you understand that test, but that's the first difference. I'm not trying to make this difficult, it is really complicated, especially for someone without the background... but you obviously have some knowledge.. it would be so much easier if I was talking to you (well, it would still take time). I'm tired now, but wanted to acknowledge your comment, but I will be back and try to explain some more.

The '7 alleles' had nothing to do with the mtDNA. Those were from the STR-DNA test. They do not use the term alleles in mtDNA testing. And yes, you did see how the mtDNA is used to way back, and it is used a lot in geneology and people doing family trees, etc. In forensics, it is a little different. They usually sequence 2 highly variable regions... and they don't try to match a haplogroup, etc. They would just use someone from her family. They do this a lot with remains, like some of the people from the 9/11 attack, they had an idea who the person was of course, and if the mtDNA matched their mother, then they knew that body part belonged to them. (gruesome, but you get the idea). But here, no one would be arguing... so here, we have the "legal" issue. No one is going to come and say, "oh no, that arm could belong to your cousin" :P. But, if you were a lawyer in court, and you wanted insert "doubt' in someone's evidence, you could easily do so with mtDNA. And of course here, the defense could LEGALLY say, well those bones could belong to 1 in 20 of the people that live in the area (or something like that, but I mean it would not be a good looking statistic) of course, for the defense, not having "a body" could mean "no murder". So while the mtDNA ID'd the body for the 'public' as Kratz said, he learned enough to know he would have this legal problem. But they were stuck, because they didn't have STR results for any decent statistics. Not the ones they gave, that's for sure.
I think (and this part is "me").. that they used the FBI statistics (as they referenced)...BUT put the with the "7 alleles from the STR".. see, they talk about the statistics in the paragraph after, so logically, just like you did , a person thinks those statistics are talking about the 7 alleles from the STR.
But the FBI didn't do the STR. The FBI did mitochondrial DNA testing. But they don't mention that at all in the DNA report? If the body was ID'd by them, why not just say that (I already told you, lol.. I'm too tired to be talking, I better stop before I confuse you ).. So, I think (this is the me part).. they intentionally used the statistics from the FBI mtDNA test, and plunked them down after the NON related STR test... so people would assume the 2 were associated. And to me, that is pretty much lying, for lack of a better word. Anyway, I will try to explain the STR test a little better, and look for some good references for you that will help. I have found some good ones that actually were made to help lawyers understand the science, you might find them interesting..... So, again the 7 alleles had nothing to do with the mitochondria.
Those were from the STR typing that she did (if you read the DNA report you will see that). There are 'statistics' with those tests, BUT they require the whole kit to be done. It doesn't matter WHICH ones match, but rather how many.
Oh and to address your one question, the defense DIDN'T KNOW they were dealing with mtDNA, because they just had the DNA report, talking about the autosomal DNA, and I guess that email... with the one sentence with mtDNA... but really, a lawyer, a layperson, would have no idea what that means, they would not even question it! Most people don't even know about mtDNA! They probably weren't in GreenBay to hear the press conference. I just think it is horrible to see science being used to deceive people. Then I will tell you a scary story how even with this 1 in a bizillion statistics.. it's still not perfect.....