[comex]

You can't extract the keys, but you can recover a copy of the entire program, which lets you do the same thing: impersonate the 'TPM'. The only difference is that, as you say, any per-user transformation of the data could be done on the user's PC rather than in the cloud somewhere - but considering the orders of magnitude of overhead the obfuscation would probably impose even if the current research is vastly improved on (though I'm just guessing), I suspect it wouldn't be worth it in practice.