Depending on how thorough the company is, the SOP with paper is to just go through the document and strike (with a pen) the stuff you don't agree with, then sign it and hand it back to them. Chances are, they won't notice. Sometimes they notice and don't care. Very rarely, they notice and do care.
When it comes up, however, if they signed it too, then you're in the clear. If they didn't read your modifications, they're no better off than if you didn't read the contract to begin with.
The problem is whether anything like this could be an acceptable way of modifying a contract. It seems to follow a similar principle -- if the service in question isn't expecting it, then you modified the contract and they agreed also, so you win. But at the same time, unlike paper, there's no reasonable expectation at this point that the server will notice these headers, and if we either insist on some acknowledgment from the server that they like those headers or wait till this is well-known enough for services to adapt, then you'd be right and they'd be unlikely to accept any changes.