Do they sell the rMBP 512GB SSD, 16GB RAM, and 2.7Ghz processor in store? I recall Apple used to sell only a maxed out configuration as opposed to a combination of all the different kinds.
All the stores sell the base models, then some stores stock an "ultimate" model that is maxed on everything. This varies by store so you will want to call ahead.
If you're referring to the Apple [Retail] Store:
Base ~ 2.4/8/256 - $2,199
High ~ 2.7/16/512 - $2,799
Max ~ 2.8/16/768 - $3,449
The Base and the High are channel configurations (you can get at Best Buy, Amazon, etc.). The Max is technically a custom configuration, but it's available at the Apple [Retail] Store.
If you're curious, the High configuration defaults to 16GB (was 8GB) now which is why it's available.
You can probably get other configurations at B&H or the one you want.
It does vary by area. It seems like often the smaller stores don't always have the ultimate models. You also might try calling again and speaking with someone else. I have found some of the Apple Store sales people are not familiar with this.