Why is the 7th[F#] the second darkest pitch, and not played on the 2nd fret of the 1st string, where it actually would be in a pitch "order" according to the scale?
You've actually shown F#maj7 - G is one fret higher. It can be, and often is - 4/5 3/4 2/3 1/2 (str/fret). And sounds good there, except the root, on 4th string, is quite high.
There is no reason at all for playing the notes in rising order rather than mixed up, although the voicing, particularly on guitar, sound not so good with an extra G right next to the maj7 (F#).
You could experiment with other voicings - as long as the root, third and maj 7th are in there, you don't even need the 5th, although it can go in, if fingers on frets/strings will allow. You'll find some (of several round there) will sound better than others. That seems to be Justin's way of preference - or possibly preference for students.
Scale degree 3>5 is a m3, 1>3 M3, and 5>7 a M3 also. 'Sounding darker' could be because of the mix, although playing just the top 3 note (B D F#) produces a B min chord - supposedly dark in its own right.
This is easier to explain in notation. All of these are a Gmaj7 chord, in different inversions and different voicings. There are lots of other possibilities too, particularly if we include 5 and 6-note versions.
The particular voicing you showed us has the F# low in the chord. Like the second and third of my examples. Several other voicings are possible on guitar, though not as many as are available to a keyboard player with his 10 fingers and two hands! Even more are available to an orchestral composer or sequencer.
So, the notes of a chord don't HAVE to stack up in close order, and very often they don't. On guitar the mechanics of the instrument restrict your choices somewhat, but there are still several 'shapes' for Gmaj7, up and down the fretboard.
Many chords can be played on the guitar with a variety of voicings and fingerings. In many cases, some voicings and fingerings will work much better than others, either depending upon the surrounding context or the dexterity of the player.
Seventh chords are usually followed by a chord which has a note at the same pitch as the seventh, or a half step down or up (dominant and minor sevenths more often resolve down; major sevenths resolve up). Resolutions are most satisfying if the note to which the seventh resolves is in the same octave, and so the forms of seventh chord where the seventh is in a middle octave can be good if the following chord has a note in the right place. Many chord charts, however, simply pick chords based upon what most people would find generally find easiest to finger (without any consideration for surrounding context), and yours may might be intended to fall into that category.
If you would be capable of playing the chord as 2-x-x-3-2-1 or 2-x-3-3-2-1 those would be fine ways of playing it (for F#maj7; shift up or down as needed for other root pitches), but I think many people would have trouble fingering that. Fingering it as 2-x-4-3-2-1 would be even better, but would probably require reaching the index finger across at a weird angle to fret the outer two strings.
If a performer can't finger a chord cleanly, it's likely to sound bad even if it should contain the ideal combination of notes. A chord which contains a less-than-ideal combination of notes, fingered cleanly, will generally sound better than a chord with a superior combination of notes, fingered poorly. For that reason, many tab sheets deliberately use less-than-ideal combinations of notes, and are not intended to discourage players who can do better from doing so.