What responsibility, if any, does the customer bear in avoiding harm to himself?

The onions in question are a burger topping, and are readily discoverable if the customer checks their order. I think that the customer with the special requirement can be reasonably expected to verify their order meets their needs before incurring harm.

I believe he's already suing Sonic for the same issue. He knew (or should have known) this was a mistake that restaurants can potentially make, yet he apparently made no effort of his own to mitigate the risk by checking his food before eating.

I would argue that it is "reckless" for the customer to blindly trust the worker fulfilled the special instructions, and that this "recklessness" is the primary cause of the harm incurred.

I would say that the restaurant's liability here is the cost of the "defective" burger.