Hi,
I have also noticed that issue. Firstly, the setup updates were not available for x64 machines and now they are all gone. If you had downloaded the setup updates before, you could now create a setup config file (e.g. "setup.xml") and point to the folder containing the *.msp file with the updates (as described in the KB you referred to). You can also now skip updating the files in order to get the CRM running by simply choosing "do not update the setup files" in the CRM installer. Doesn't that help?
Kuba