The constant generation of new balnace-holding addresses on demand, that are not typically shown to the user unless they dig, is an arbitrary choice of the Bitcoin-QT software, not a requirement of the protocol. In the protocol/blockchain, you can see every public key that has ever received any balance. You can have all your 'change' returned to a small set of pregenerated/registered addresses.

So the government just says, "Here, use one of these 12 wallet programs, they are certified as automatically compliant by the IRS. Using other software makes compliance your own headache."