But the patents don't cover the process of making the files available to the public via HTTP supported by ads -- it would appear that these restrictions on that are a novelty of MPEG-LA's standard contracts for licensing the patents.
They're obviously enforceable on the organizations that entered into those licensing agreements directly, but what if I bought an licensed encoder off the shelf?
Is the on-disk format itself somehow patented, such that the files themselves are patented articles? Wouldn't that fail the machine-or-transformation test rather egregiously?
No no no, you're making the assuption that "buying an licensed encoder off the shelf" gives you some kind of patent license. It does not. It's a license to run the software from the manufacturer of the software. It sometimes contains a transferable license from the patent holders, for some purposes. Read carefully.
But walking into Fry's and buying a codec product off the shelf for $49.95 doesn't automatically allow you to start a video megasite.