When a plug is not inserted then pins 2-3 and 4-7 are shorted, when you insert the plug then you use pins 1,2,5.
2-3 and 4-7 are not bridged when the plug in inserted.
This bridge 2-3 and 4-7 is usually used to feed the signal in a device like a speaker when there is no headphone plugged and when you use the headphone the bridged pins disconnect and the sound doesn't reach pins 3 and 4.
The phone line is normally the red and green wires. Additional lines/features go on the black and yellow wires.
You speak of connecting the mp3 player directly to a RJ45 connector. Do the instructions say anything about 60 volts being on a phone line when not in use? Do they say whether an inline capacitor is necessary and sufficient to protect your equipment? With no capacitor your mp3 player will be okay as long as your phone is off the hook. However when you hang up, 60 volts will suddenly go to your mp3 player. You should test with a voltmeter as to all situations.
That's how I've understood it since 30 years ago. It may or may not apply to you, depending on local phone company setup, etc.