I have the new files format setting, setup to create files in Unix format. If I open a new file from the icon bar 'new file icon', this has the desired effect: a new file in Unix format.
If I open a non existing file from a command line (cygwin in my case), NPP offers to create the file as new. It does this, but always seems to make it in Dos/Windows format.
Work around is to manually switch, but I often forget this and then get wrath from my Config Manager about submitting DOS format files :-(