Hi Diki,
Yes, it is certainly more natural to use the Chord Sequencer. As you said, this offers greater flexibility and spontaneity.
I would assume a professional player would prefer to exploit the advantages of a Chord Looper.
The auto tracking of Chords embedded within an XF MIDI file is more of a learning aid for beginners to help them learn a new song.
Now they don’t have to worry about playing the correct chords while trying to master the melody line.
Without the auto Chord Tracking, the beginner will be stuck on hearing their favorite Style play on the C Major chord which may sound rather discordant!