I have a Trigon-6 desktop unit (serial number 193). And I do think I observe some of the behavior you are describing. I was working from home today, and my keyboards are perilously close to my work space. So I tested the Trigon-6 throughout the day with some power cycling, some recalibration, and some indiscriminate jamming because it just sounds so good. I tested the tuning with an app on my iPhone (Tuner T1 Pro). The tuning of oscillator 2 did seem more often to be a bit high compared to oscillators 1 and 3. The app has a "green zone" indicating "in tune" and the 6 voice cards with oscillator 2 would sometimes be just north of that green zone sometimes when the other 2 oscillators were still "green".
To my ears (without the app involved), it still sounded great. I absolutely do not have an ear for knowing if things are in tune and exactly on the precise note. So I can imagine (well, okay, I am certain) that I don't realize when tuning is slightly off. But, on the other hand, I really love the sound and suspect that might be due partially to the inexact nature of the tuning.
It was definitely an interesting exercise, and it does seem you might be on to something. As a result of this, I will be a little more careful about checking the tuning now when recording an audio track. But I also would not want for anything to change with the synth. This variability in the tuning of these instruments makes me a little bit happy.
I'm glad you started this thread. I will keep my eye (um, ear) on it a bit more closely and see/hear where it goes.