The RAW files are simply files … you can also copy them by hand from the CF to a certain folder on your hard drive. So as long as a so called "transferring program" is only copying the files, nothing happens.
However there may be certain softwares that read/write Exif Data (and therefore in fact change the original file)… I don't know. AFAIK Photomechanics does, but again, I'm not quite sure.
Once used to the workflow in C1 you will most likely use the importer tool of C1 anyway (actually this is also the easiest way to start with).
demosaicing happens when you open the file in C1. But only for the preview - the actual RAW file remains unaffected; C1 is totally non-destructive, i.e. all adjustments are stored in separate setting files, but not in the actual RAW file.
The actual pixel file (JPG or TIF) will be baked when you hit the "process" button…