I think there were some changes to the file format, possibly due to the 16bit color ability. maybe just to lock Lr out. I'm guessing Phase isn't being helpful as they see Lightroom as a competitive product. (Trying not to step too far out of bounds here, but this is actually not a total guess).
Personally being forced to use C1 all of the time is something I'm pretty uncomfortable with, as C1's automask tool is terrible, it's HDR sliders are not nearly as effective as those in Lightroom (not sure about everyone else, but the Shadow slider to me is more like a shadow/midtone slider), the local adjustments as layers are nice but are more difficult to work with.
I realize Lr competes with C1, but when you spend the kind of money it takes to get into this system, I think phase should be pretty happy and not worry about the fact that you aren't using their $100 piece of software. Sort of sours me on them a little more ....
Not sure if we could get enough of a grass roots movement to push phase in the right direction here so Lr (and Apple for that matter) could handle the files.