Equal temperament is definitely a compromise .. I find myself constantly trying to "sweeten" the tuning of my guitar strings relative to the song/key I am playing.
You can tune your guitar with the most accurate guitar tuner in the world (I have strobe tuners by Sonic Research and Peterson), and some things still just sound out of tune.
That doesn't sound like a description of a problem with equal temperament. In fact, the whole point of equal temperament is that any given chord has precisely the same tuning in every key. Isn't the purpose of these staggered frets to tune the guitar to more accurately match equal temperament? In other words, a guitar string played on the 7th fret is supposed to be tuned exactly 7 12-TET semitones above that string played open, but with completely straight frets (in lines exactly perpendicular to the strings) it's difficult to get every fret on every string to be accurately tunes.
I believe this is what's referred to as intonation. Many guitars have some form of manual adjustment, like a movable bridge saddle for each string, and it's common to use that to slightly adjust the length of each string so that e.g. the 12th fret is accurately in tune with the open string. These "true temperament" guitars seem to have done a similar thing but with small adjustments to each fret on each string. Presumably the fret arrangements are designed to match that exact guitar fretboard with some specific guitar strings?
The article says "with a normal guitar, if you play an A Major chord, then play a D Major chord, those chords will be slightly out-of-tune with each other." Again, this doesn't sound like a description of a problem with equal temperament. From what I can tell, these "true temperament" frets would help specifically with playing the same chord/interval in different positions.
I'm not crazy about the sound, myself. It's kind of like a guitar sample played through a MIDI keyboard.
From the small clips I've heard, it sounds great to me, especially when the guitar is playing alone. Back when I played a lot of guitar I was often pretty bothered by intonation issues, even with decent gear that was setup well and didn't seem to bother other (much better) guitarists. But of course guitars often play together with 12-TET instruments that are likely to be much more accurately tuned (like a piano or organ), and it makes sense that the every-so-slightly out-of-tune nature of guitars has become part of what sounds distinctively guitar-like, especially the specific tuning you're likely to hear a lot with common guitar chord voicing in many styles of music.