a sequencer is preferred because it's easier and quicker to create your music
a tracker is just hard to read
The difference between a sequencer and a real tracker (eg famitracker) is like the difference between making a game with pixelated graphics in game maker, and making a real NES game in 6502 assembly. The previous one is easier, but it doesn't really require any effort, and usually ends up pretty characterless. The latter one is more difficult as you're confined to the hardware limitations, but it's so much more authentic.
I despise any chiptune music made in sequencers; infact, I even refuse to acknowledge it as chiptune.