Basically, this is the way Lightroom works ... correct one profile and apply it to all as a sync batch ... or am I missing something?
I suppose changing the default to the S2 profile would be okay if you only use C1 Pro for S2 files, otherwise I'd just apply it as above.
Jury is still out as to whether this profile offers enough advantages over Lightroom by applying user defined camera specific adjustments. The vast level of tools in lightroom, direct access to photoshop and third party programs like Nik Define 2 and Silver Efex Pro without leaving Lightroom, make it difficult to move elsewhere for processing except in very critical cases.
What we do not know is whether this new profile is any better than the embedded camera calibration provided in Lightroom. I understand that the new profile opens up the S2 to those who prefer Ci and are proficient at using it, but I seriously doubt it is the same as using C1 to process Phase One files (or Phocus for Hasselblad files).
IMHO Leica also needs to have Adobe juice up the S2 camera calibration options in Lightroom. If I recall correctly there is one embedded one for the S2 and fourteen options for Canon. To be perfectly honest, the red bias in the skin tones needs to be addressed ... if there is anything that is a PITA when processing S2 files, it is that.
-Marc