I don't believe the differences you are hearing is due to MK1 vs MK2 but rather tube (Unless you're swapping 1 tube between the two) and/or caps within the T1 itself. The caps vary wildly from device to device even within MK1. Comparing internal shots, there's very little difference besides the USB reciever change (sync to async) and caps.
I'm indeed swapping the same tube between two, using same headphones, same system to do the comparison.

The comparison is base on stock tube EH 6922, Tesla yellow label code 32, Amperex bugle boy E88CC, Siemens E88CC A6 and Mullard ECC84 with adapter (Philips label).
Other than that, didn't touch anything including the caps that you mentioned. I'm not a technical person, not so familiar with the circuit design and didn't open up the unit to check.
Sometimes base on internal shot, it's also quite hard to judge whether the sound is the same. For example, you won't know whether they are using the same welding tin or interconnects or any other tiny parts.
So far, I happened to audition a few units of t1 mk1. The sound won't vary that much and they are with the same sound signature. If the difference is due to caps that you mentioned, they should all sound quite different.
I kept T1 mk1 and mk2 together for comparison for more than a month. A friend of mine who is a classical fan and pianist, know nothing about Aune, bought over my T1 MK 1. He also managed to hear the difference as well and prefer mk1 over mk2. I keep MK2 because I like the sound signature and mainly listen to pop, rock, new age, vocals and electronic.
Of course I won't know whether the difference is due to different batch of Aune T1 mk2 or not. Sometimes, for some gears, even under the same batch, sound slightly different from one to another. So far, I didn't find that on T1 mk1.