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I think there are too many variables to say, ie; do the cc terminals at the stores query the same backend as the online webapp? its concievable that they do but who knows how much of the application process is infulenced by costco and if those systems process those apps separately. I`d guess that the reason you can get a 2 for 1 application on the website is because AMEX stores the last hard report on their DB server which they are probably contractually allowed to store for $X days and when you submit a new application the web app checks to see if they already have a report for your SSN and make the decision based on that.
Its a toss up, perhaps you just need to take a deep breath and hit submit Whatever you decide good luck!
I think if you don't mind the 2 inq, you should go for it, that way you won't be upset with a surprise. I don't think there is anyone who is going to know for sure, especially when the customer service can't even really tell you, just one of those things.
I was just recently approved for the Zync, and I did my application on the computer, then later in the day applied for the Blue Sky Preferred on the phone, and it was 2 inq. So, that's just my experience, hope it helps you out.
I applied for 2 cards on the same day. A Business platinum and a personal SPG. The business platinum was approved and of course there was an immediate hard pull on my CR. I got the 7-10 day message on the SPG card so I waited. When I didn't hear in a week and the app kept showing as "in progress" I called. The rep told me that the second app was canceled as the computer will sometimes due that when there are multiple apps in a day thinking it was an error. Ultimately, I was declined for the second card (I already have a personal platinum and the Jetblue card) but I noticed the next day that they had pulled my credit report again. So I sent in 2 apps the same day and ultimately got 2 pulls and only one approval. Just my experience.