I confess to not having followed this discussion very closely. I thought around 500,000 years was the agreed limit – what are you basing the 700,000 years on? (Just curious.) Obviously, all of these numbers are somewhat mushy. If you accept the estimated time of 700,000 years for the sapiens/Neanderthal split, then that’s your limit, of course.
Not exactly my area; I was an author of the chimpanzee genome paper, but my contribution was in modeling selection, not in the sequence comparison. On the other hand, I am pretty familiar with the paper, and it’s safe to say that the quoted text is completely wrong. Similar claims have been repeatedly introduced into Wikipedia, where they have have had to be weeded out.
Short summary of the actual comparison:
2700 million base pairs (out of a total of roughly 3100 million bp) of the chimpanzee genome was sequenced well enough to be compared. That is the portion we can say something about. Of that 2700 million, 2400 million could be aligned to the human genome. This portion is the basis for the conclusion that 1.23% of sites in shared DNA differ by a single-base substitution, and that another ~1.5% was unique to each genome. (Based on these numbers the most reasonable single statement of overall similarity is that approximately 97.3% of the human genome is identical to the chimpanzee genome.)
The remaining 300 million base pairs of chimp DNA was sequenced but was not compared. 240 million bp were left out because they aligned to multiple places in the human genome. Much of this (I don’t know exactly how much) was the result of badly assembled chimp DNA, while some may represent genuine duplications in the human lineage. Another 90 million bp didn’t align to human at all; again, most of this was probably garbage of various kinds – badly assembled chimp DNA, parts of the human genome that hadn’t been assembled, etc.