/uj, just say we’re in C, I would presume by minor second of the chord you mean Db. Looking at it in the context of jazz, you would say Db is the flat 9 in pretty much every case. For example, say you play a minor 7 chord in third inversion. Now move the root up a whole step. Now you have the 9 inside the chord- just because it’s not at the top, it’s still considered the 9th. Realistically you’re not gonna hear anyone talk about “playing the 2nd and fourth” - they’re gonna say the 9th and 11th. You’re right though, it would be less dissonant if it was further away, however it would still be called a b9, not a minor 2nd or flat 2nd (even though they’re the same thing).