Maybe it is a geography thing, like California taxpayers who owe $500,000 are not assigned to an RO but Nebraska taxpayers who owe $100,000 are. I don't see 200 pages of documents on a house sale, but I often see 20, and often one of them is the form that the escrow company supplies to the seller asking them to sign if they qualify for the 250K/500K exclusion. Maybe they should not be doing that for any sale over 250K, but in my neck of the woods they are, and when I see it I don't see a 1099-S. And I don't report the sale on the return, and I never see a CP-2000.
I have been paying someone for the last 20 years to answer the phones and tell callers we are not taking new clients. The old ones just keep coming back. I have enough work to do, helping them with forms that IRS requires, that I don't waste time on forms that are not needed. I am sure that the AUR program has some criterion before chasing after a 1099-S report -- maybe when the proceeds are more than a million dollars. But then, they might have some criterion for chasing after a change of address when mortgage interest is being deducted.
I will be sure to let you know when I see my first CP-2000 or CP-2501 for a return where my conclusion was that no 1099-S was issued. Meanwhile, the fact that you saw one in 2008 doesn't mean that IRS hasn't since figured out they have better things to do.