Both are the same spec, except for the firmware. The Borders units will point you to the Borders store.
If you want to use the Kobo bookstore, you can simply 'convert' the unit to be a Kobo unit by syncing with the Kobo desktop application. After this sync, it will always sync / connect wirelessly to the Kobo store.
I.e. you can go buy the discounted Borders unit, sync with Kobo desktop and it's now a Kobo unit at about half the price
