The biggest issue with plain layer offsets is parallax won't work with them.
It may have to be parallax, or offset for all layers, not both, and probably not alternating either.
That's not true, they can work together. Imagine that the offset is an independent parameter that maps to the amount that the layer offsets from the scroll position, like: "layerPosition = layerScrollPosition + layerOffset". One can then have the layers move with scroll plus control the layer offset, or can alternatively set the scroll rate to 0 and move only with the offset without being affected by scroll.
The only thing is that the offsets need to be taken into consideration for the collision cells like Ashley mentioned. Apart from that it seems quite trivial to implement.
I felt the need for this feature sometimes in the past. Although it's not something I'm really in need for C2 right now, I really wish to see this in C3 as it would be very handy.