The roots will work their way through the shallow part of the clay soil and spread that way. Think of the setup initially as a self irrigating pot.
I would not want the trees to be bound on all four sides unless the edges of the raised garden are shallow themselves, allowing the roots to keep going past the boundary, otherwise it'll be as if you planted your trees in a barrel and the roots will stop spreading at some point. This is not going to happen immediately, but two or three years (perhaps longer) down the road you might end up losing your tree if it becomes root bound.