Most grassroots nurseries (like mine for instance!) will honor box store prices with a better selection!
Not in my neck of the woods. I have to drive half an hour (past probably 20 local nurseries) to beat the HD that's 5 blocks away. That's for price, selection, service, return policies etc. Quality is arguable. I've gotten trees from HD that declined rapidly, but have also purchased much more expensive trees from local nurseries that declined. Recently I was looking for mexicola avocado, which I hadn't seen in 3 different local nurseries. But when I wandered through the trees in HD it was there, for $12.
I say shop at the stores with the best quality, service and selection.
If you stop buying the more unusual trees at costco etc., you're also signalling them to stop carrying the more unusual trees and ultimately limiting the exposure of non-experts to those trees. Weren't we discussing some mango on another thread that big nurseries wouldn't carry because no one would buy them? If you do buy the unusual trees, then you increase the chance that the stores will continue to carry them and branch out into even more unusual trees.