On programmable device, each layer of a programmable interface, for a protocol which has a protocol stack including at least a physical layer, a data link layer and a transaction layer, is selectably bypassable. When a layer is bypassed, all other layers downstream of that layer also are bypassed. In addition, the interface may be divided into different clock domains running at different clock rates, reflecting clock rates within the programmable device and outside the programmable device. Layers may be bypassed to allow a user to substitute a custom layer in programmable logic, or to substitute an updated layer for debugging purposes.