So you're telling me a lightning port version of Apple's earpods would be at the same quality as the existing 3.5mm headphone jack ones?
Sound quality of music depends on so much. With regard to Apple's earpods, yes, absolutely: The quality of audio from the earpods using 3.5mm would be exactly the same as the quality of audio from the lightning port version.
Work backwards from your ears. The speaker in a headphone is analog. At some point, digital music data must be converted to analog. Does it matter whether it's a chip in the iphone doing it, or a chip in the headphones? The only thing different is where the chip is.
Working back further, before the analog audio goes to the speaker, it gets amplified. This is about power. For the power rating, the one in the iphone is already very good. For earpods, more power does not mean better - indeed more power might mean worse. For much bigger headphones, more power does mean better, but many of those super expensive super niche headphones already have special amps anyway. For 99% of users that just use plain earbuds or regular headphones, this makes no difference.
Working back further, before the analog audio is amplified, it is converted to analog from audio by a DAC. The DAC in the iphone is already one of the best mobile DACs out there. Unless you're willing to carry a brick the size of a deck of cards or larger with you, it's pretty much the best you can get. No third-party headphones will improve on this in any significant way (unless, as I mentioned, users are willing to carry an additional large device).
Working back further, before the digital audio is converted, it is read from a file. Most users listen to MP3s, or itunes downloads, or spotify, or something of that nature. These files are compressed to various qualities. For most people listening to 128kbps or even 196kbps compressed audio, fancy DACs, amps, and headphones won't make any difference whether it is over lightning or over 3.5mm.
So yes, with earpods, all other things being equal, lightning or 3.5mm makes no difference what so ever.
The only scenario that I can think of where lightning might be better is if the user is listening to a lossless file, the user is willing to carry with them a big external amp and DAC, and the user is listening on expensive audiophile-grade headphones or earbuds. What percent of users do you think fit that profile? Maybe 0.1%? Even that might be generous...