So here's the interesting thing about whether the Apple website shows the product in stock or not. I was debating upgrading my Gen 1 12.9 iPP when the new models came out, and I went to the local Apple store last week to check out both the 10.5 and new 12.9 models. Online inventory showed both in stock (was looking for Space Grey, LTE, 512GB). I ended up buying the 10.5 model, but after a week of using it, decided to go back to the 12.9 form factor. Check online at all of the local Apple stores to me, and all of them show delivery dates in mid July for Space Grey, LTE, 512GB models. One store showed the Silver, LTE, 512GB model, so I stop by the store and try to convince myself that Silver suits me just as well as Space Grey.
When I'm talking to the Apple store employee about picking one up, she offers that they have all of the colours in stock, and if I want Space Grey, I can get Space Grey or Silver, or Gold. So despite what the online inventory said, they had several 512 GB, LTE, Space Grey models in stock in the local Apple store I was in.
It appears as though inventory for walk-ins may not factor into the published inventory for the online order and pickup in-store process, as I have my brand new 12.9 iPP with me now.
If a store is close enough for you, it may actually merit checking out whether they have inventory set aside for walk-ins vs pickup orders.
Patrick