Of course it will be a little more. I always have the thought process that what I am paying for is their experience first and quality second. Meaning they know how to help, answer questions correctly, and always cull out the bad lumber or products which do not work well. They want to keep your business rather than sell volume.
I get actually have a contractors discount of 12% and billing at the end of the month with my lumber yards. If I pay before I get the bill, they add another 2%.
With a $100,000 addition...that saves me...??? never was good with math, that's why I'm a carpenter.
It all depends on where you live, and the volume you buy, for homeowners I would guess about 5% more. But work with them and talk to the owner if you have to. Granted they will never be lower than the box store, but they should reward loyalty.