by all means the proper way to orient a cut nail is with the grain of in this case flooring. The same is true no matter what medium that you are nailing to one another usually it is the surface cladding that the nail stays oriented with the grain.
To answer your question about what the term-- "Butt Cog" refers to well here is my explanation.
In Traditional timberframing the "Butt" or the lower end of the rafter that sits on the Upper plate usually stays in its place due to a "cog" fashioned on the end of the rafter. This "cog" has a 90 degree leading edge that sits down in a mortise usually about 2.5" from the exterior edge of the plate. This cog sometimes extends across the full width of the bottom of the rafter but not always.
after the rafter has been set in its place it was usual to use 4 or 5" spikes or a wooden peg to hold it in its positon.
Thanks for coming on board with those pics of the barn, one thing that struck me was the resemblance of the barn to a Schoharie Dutch barn with its main entrance doors in the end of the structure.