Yes, you are missing something. When you say, "With apple pay, vendors can then explicitly choose to accept visa, mastercard AND applepay" is incorrect. That statement makes Apple sound to be a type of credit card, when it is not.
The store just needs to accept NFC payments, the credit card module that has a symbol that looks like a sideways wifi bar signal. If they have this, they accept apple pay (as well as google wallet and whatever else uses NFC). They can't exclude Apple Pay without excluding ALL of the NFC payments out there.
I don't know where you're located, but McDonalds, for example, has these modules in probably every store in the USA. Therefore it was easy for them to say they accept apple pay. they've had these machines in their restaurants for a long time. Because they accept NFC payments, that's all that matters. They can't accept NFC while excluding Apple. It's all or nothing.
It comes down to this... These stores aren't explicitly saying no to Apple Pay. Instead, they are saying no to accepting NFC. By them calling it apple pay just goes to show how powerful apple is in entering an industry, already using their coined term for the technology.
So when Costco says no to apple pay, they're really saying no to NFC machines altogether.
In a way, Google Wallet has helped put these machines in a lot of stores. The difference for us is that Apple Pay is a more secure way of doing it. Google will keep track of where you buy to keep profiling and making advertising dollars off of you, Apple won't. Google will be using and sharing your credit card number with the store, Apple won't (since it's a one time use card number they use each time).
You almost got it right. Google doesn't share you CC number as you're given a virtual Master Card number and each time you make a payment a token is generated for that sale.