Lots of your customers will wind up with store.yahoo.com/yourdomain urls in their bookmarks, even if you own your own domain.
I bought a business that had a yahoo store last year (my other sites are ecommerce, but not yahoo). The business had its own domain. We set up our own site but we have had to keep the yahoo store up because so many people kept going there even after our email notices.
As far as I can tell from traffic analysis, we never benefited by having a yahoo store.
"does being in a Yahoo Store get you access to some traffic (or a headstart on good traffic) that an outside store misses?"
From my understanding the only difference is that with a Yahoo store you get listed in Yahoo Shoppping.
There was some speculation when they first started charging the 3.5% commision from the Yahoo network that Y! stores would get preferential treatment in the directory. But that doesn't seem to be the case.