'Motorola's devices on the other hand will likely be significant departures from Intel's reference design.'
'Lenovo's K800 is based on Intel's FFRD although with an obviously customized chassis and software stack.'
'Intel's belief is that by delivering a reference platform that can actually be used and sold, it allows its customers to focus more on software/differentiation, rather than building a reliable, well tested smartphone motherboard.'
Finally don't forget phones sell as much on design as they do on internal chips. They all currently have roughly the same ARM chips yet the phone makers have found ways to differentiate on other features. The reference design just gives a ground zero design to start with that some may choose to finish with.