Alex was completely right that it’s very hard to subjectively compare two outputs that have different volumes and people have to take that into consideration when reading my comments. I’m not pretending to be scientific about this, there’s no blind testing, and I’m volume matching by ear.
That said, I’m listening specifically for brightness and/or too much energy in the highs (in case there’s a technical difference between the two). Out of the box, using the same single ended cables I use on my Pendant, Lyr 3 and Soloist 3XP, the Jot was much brighter than the other amps. Too bright for my taste, which may be different from others, but then I bought it for my use, so my taste rules. 
I just played snippets of Funkadelic’s “One Nation Under The Groove” (from the namesake album, the 1993 Charly edition for those that want to replicate it) for what seemed like 100 times, comparing various combinations of cables, outputs and amps. The track has a lot of treble energy, which was really all I was trying to focus on, because I am sensitive to brightness, and I was “measuring” the relative brightness by seeing how I reacted to the cymbals and guitars. I even turned the volume of the SE output up so that it was louder than the XLR output, just to see how my brightness radar reacted. Again, not making any scientific claims that this was the correct thing to do.
I first listened to the Soloist 3XP to give myself a baseline, on both SE and XLR out, and then did the same thing on the Jot 2, using the same cables. The Jot was overall brighter than the Soloist, and the XLR outputs seemed brighter than the SE outputs. I tried this with my Stellia (low gain), Verite, Aeolus, 6XX (all on high gain). The differences were smallest on the Stellia and 6XX.
I also tried switching between high and low gain, and the sound was less bright using low gain, but I didn’t enjoy the overall sound on the Verite, Aeolus and 6XX. The amp seemed to be more in control of those headphones when using high gain, which is consistent with what I’ve found on my other Schiit amps.
I tried a Pangea XLR cable, first to the Soloist and then to the Jot 2, and got the same results.
At this point, I stopped comparing amps and started switching cables on the Jot 2.
I switched the interconnect from my fancy Furutech OCC copper cables to Schiit Pyst and some of the brightness went away, but it was still there. The differences were smaller but I still heard them, and I had consistent results on the same 4 headphones.
I switched to my old Van den Hul “The Second” cables and the brightness went away, so I’m guessing that the VDH cables are acting as a treble filter. The Jot 2 now sounded wonderful to me, very balanced, so I could focus on all the music instead of just the highs. The treble differences were tiny, but still there if I was actively looking for them. But what was more apparent now was a smoothness in the vocals on SE that wasn’t there in XLR. I went back and forth multiple times and heard it quite distinctly. It was interesting, the XLR output had a little more of an “etched”, very detailed character to the vocals, and the SE was smoother but still had a 3D presentation. Neither was better than the other, just different.
Using my Van den Hul interconnect cables, the Jot 2 sounds perfect. Vocals and instruments have a 3D texture that’s missing from the Lyr 3’s flatter presentation. Bass is full and controlled. The amp has rhythm, judging from my foot tapping. There’s a ton of detail in the music, much more than the Asgard 3 that I recently gave my son. My powered Emotiva monitors and sub also benefit from the detail and texture of the music.
I was looking for a solid state amp for headphones and also to connect to my monitors, and I had to choose between the Jot 2 and an Asgard 3. I’ve decided to keep the Jot 2 in my SE setup.
Since my Soloist was still in its trial period, I was hoping to send it back and keep the Jot 2, but I’m keeping both because to my ears, the Soloist sounds a little better - a tiny bit more holographic and 3D, a little smoother and it doesn’t have the brightness of the Jot. Physically, I don’t have room for both the Jot and the Soloist, so I’m going to move the Soloist to another area on my desk, to start a new fully balanced setup, as it sounded really good using my new XLR cables.
I know that it looks like I focused primarily on the highs, but that’s what stood out to me the most as far as negatives go. Everything else sounded just right, irrespective of cables, SE, XLR etc. It might be that I’m more treble-sensitive than others, in which case it will be a nice plug & play for those people. I’m just happy that I tinkered with it enough to enjoy all it’s qualities. It’s unfortunate that Schiit made that “best $2400 amp for $400” claim because it distracts you from the fact that it is a tremendous value at $399.