What the manual means is that you can transfer standard MIDI song files and Yamaha MIDI style files back and forth between a computer and the keyboard's internal storage memory.
However, when you record a user song the keyboard saves it in a sort of abbreviated MIDI format, presumably to help reduce the amount of overhead needed and thereby fit more data in the internal storage memory.
In particular, the header chunk that's at the beginning of every standard MIDI file is omitted, and the settings for the song are stored elsewhere as part of the keyboard's normal backup data.
If I remember correctly, the song tempo or MIDI clock rate is reduced by some factor, presumably so the delta times between the MIDI events can require fewer bytes, especially for any lengthy pauses between events.
And the MIDI track data is split into blocks of memory, the way computers typically divide storage memory into blocks of data, such that a given track might take up several blocks of memory, but each block of data is not necessarily contiguous to the other blocks and the blocks are not necessarily in sequential order.
On the models of the 400 series, the "Save SMF" function writes all of the song data to an actual standard MIDI file, converting the song settings into a header chunk and then creating the track chunk with the proper delta times for the specified tempo and with the data from each data block written out in proper sequential order.
Since the 300 series doesn't have that "Save SMF" function, the equivalent conversion process would need to be done manually by saving the backup memory to a computer and using a hex editor to extract the song data and assemble it in the proper format and order, including the creation of a header chunk, then saving the song data as a standard MIDI file.
