Although true, I doubt that's the reason since stuff like this was common pre-ACA.

The truth is that everything that a payer pays for is done through contracts. Payers will often default to a specific provider because the contract covers it and they don't have a contract for other providers.

In terms of the cost, back-end rebates often bring it down. Also, this particular contract may cost more for a flu shot, but save them even more for other procedures.