The RCFile implementation was copied from Hadoop's SequenceFile and copied the 'magic' string in the header. This means that you can't use the header to distinguish between RCFiles and SequenceFiles.
I'd propose that we create a new header for RCFiles (RCF?) to replace the current SEQ. To maintain compatibility, we'll need to continue to accept the current 'SEQ\06' and just make new files contain the new header.