Because I am a believer in the traditions of science, yes, I think it would be an excellent idea if you wrote up formally your problems with his paper...
which I *promise* I'm going to read, tonight while I wait for a server upgrade to finish. :-)
And certainly any level of the stack can be attacked, and I understand that was his point. But one either has to say "there's no practical way for me to validate the microcode of the CPU, and thus there's a practical limite to what I can verify", or one has to -- in fact -- do that validation.
If one can.
As we note on RISKS regularly, there are two issues at hand here: "pick your own low-hanging fruit", ie: make sure you apply extra security balm equally to all layers of your problem (as adjusted by your threat estimates at each layer), and "know your CBA": the amount of security at all levels you apply has to be in keeping with not only your threat estimate, but with what the bad guys can *get*.
This is, in particular, the part of the issue that terrorists throw monkey wrenches into: trying to inspire asymmetrical responses to what are, objectively, low-level threats. Your opponent wears himself out on the cape and never sees the sword. Bruce Schneier likes to address this issue.