Historically speaking, the overtone/harmonic series is probably why we hear them as R-3-5-7-9-11-13. That's the natural order in which overtones occur, and it's actually the discovery of each partial that led to the evolution of music in the early days. A semitone wasn't a common interval in a melody a 1000 years ago.

But your post raises another point: Chord names are not literal instructions for how to voice a chord.

Cmaj#11, for example, is palette of tones you can choose from: C-E-G-B-D-F#.

You don't need to play all of those notes, and it's actually a very guitaristic thing not to. If you're playing with a bass player, you can voice chords without the root. The 5th–if unaltered–adds very little information to the chord. You could play the 3rd and 7th of every chord and totally hear the changes (this is fun to do with a blues, since you're literally moving a tritone dyad by a semi tone to achieve all your chords). The 9th and beyond colour the chord in tasty ways. There's no rule saying you can't voice the chord with the 9th in the bass–as in a 7b9 chord.

In the Jazz Theory Book, Levine suggests that chord symbols are synonymous with scales, which I like. Cmaj7, in the context of the I chord, is just C lydian (R-3-5-7-9-#11-13). So Cmaj7 can mean Cmaj9, Cmaj13, Cmaj#11/D, etc etc.

If you're looking for an exact result, then indicating the inversion (with a slash chord) and including a melody note will make most well-trained guitarist play exactly the chord you're looking for. So for example, if I see a B in the melody and a Gmaj7/D chord symbol, that really narrows down what to play.

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