When Harry Smith put together the Anthology in 1952 everything in it was supposedly out-of-print and one of the reasons that Folkways got away with releasing what was then essentially a bootleg was that the companies that then owned the masters didn't care at the time.

This is just me thinking out loud, so don't take it as gospel, but perhaps the Rodgers material was in-print at the time (although I'm surprised that the Carter Family stuff would have been out-of-print and not the Rodgers).

BTW, when Smithsonian Folkways reissued the Anthology a few years ago, they did it in cooperation with all of the record companies who owned the rights to the original masters.

Another theory I would offer is that Harry Smith was a total eccentric ant everything he did made sense. Try watching some of his films.