No need to justify. Playing with the EQ's to get YOURSELF a better sound is fine. Just as long as you realize it's not actually better. It's the exact same song. I can say "well I like hearing songs through AM radios, so poweramp is better because I can do that". Doesn't mean the song sounds any different. You're putting a mask on it.
I took issue with the person saying that sound quality is different between apps. That's flat out wrong. If you have an app that you can toggle presets to get a sound that's better for you, more power to you. As long as you realize you're masking the song, not making the song sound better. If you put things through a compressor, they'll sound tighter, but not as accurate to what the song is SUPPOSED to sound like (which will be difficult to achieve on an MP3 either way).
And of course "the difference was noticeable" between high end and low end headphones. Are YOU serious? Are you implying that the difference ISN'T noticeable when you don't have fancy EQ'S? It's always different, no matter what headphones you have. Thus my saying EQ'S are irrelevant. A good pair of headphones will represent the sound file the correct way. If you don't like that way, then you'll need EQ's. I know the dev of Lithium, and I know the dev of a knew app called justmusic (not out yet)... I know for a fact they don't mess with any magical preamps to make music sound better on their apps. That's preposterous.
My initial comment was against someone who said the sound quality wasn't as good on one app as it is on some other apps. That's flat out wrong. It's the same quality. If you're saying EQ's make the sound better, well, more power to you, I'm sure you like it better. Still the same quality.