If I am understanding this correctly (starting off from Todd Wilcox explaining that the problem is specific to the guitar's design, not equal temperament per se, that guitars especially have marked intonation problems), this here looks like a solution:
True Temperament guitars, aka "squiggly frets"
Those guitars do not have straight frets, but rather oddly shaped ones, to provide a perfect(1) position, per string, to produce the correct note.
Higher up the neck it looks somewhat like "fan frets", but on the lower frets they are no straight "rulers" anymore but go back and forth.
Apparently this is fairly new and only expensive custom made guitars are available.
Here are electric guitars, which are most known for this:
I also had a few google hits on acoustic ones with such a neck, and the true-temperament company seems to sell them for luthiers to fit them on guitars.
But the google hits for specific guitar makers and products were only in the cache, the sites apparently don't have them anymore.
But it is apparently viable. The guy from the first video, Mattias Eklundh, plays his electric models with those frets to this day, and while his eclectic style may not agree with as many as some vanilla acoustic playing, you can see/hear the guy can play:
Freak Kitchen, fusion oriented(?), ~ 2015
Fusion, "Math Metal"
Overall, Eklundh makes comparably heavy use of "harmonics" (in those E-guitar playing styles, meaning that the string is struck in a way that makes an overtone predominant in the timbre, as opposed to the fundamental), which works so well and sounds so right, as he explains in some of his videos, exactly because the usual intonation issues that would prevent this from sounding good are not present in his guitar.
(1) "perfect" with regards to reaching e.g. equal temperament, which is not achieved on every position of a regular guitar