This has been my experience as well - even down to the preference for low gain - except I skipped Jot2 and went straight to the SA-1 from A90.
Prior to A90, my only exposure to amplifiers was L30, Liquid Spark (which I really like a lot for the $80 I paid), and BasX-a100 and despite waddling only in entry level gear, I was never impressed by the A90. Using primarily Arya and Elex, I gave A90 time to burn, got a new DAC (Ares II), and switched to all balanced connection but I could not get over the flat sound that lacked contours. When I first plugged in the SA-1, it sounded like how I imagined the A90 to sound.
Fed by Ares II via balanced, SA-1 is powerful enough, even for my HE6SE V2. With the Arya, it usually stays between 2-3pm on low gain. It gets plenty loud and dynamic at this volume. HE6 is around 5pm and maxing out the SA-1 (~5:30pm) on low gain gets to "too loud but not painful". Like you, I didn't really like the sound on high gain but didn't realize why.