Lewm,
I haven't heard the new MkII but observed the same things you cite. Having spent quite a lot of time with the 2.0 > 2.0SE comparison and listened to some of the company's amps, and knowing Jasmine's track record for making content improvements when claimed, I completely trust that the Mk II is not regressive relative to the SE. The differences between the initial 2.0 and the SE were materially slight but discernible sonically. That the essential circuit is not changed works for me.
The designer has proven across his electronics product line to be worthy of being taken seriously. He voices his electronics for startlingly good music performance, especially considering price, and does not skimp on build quality nor parts. There are many reasons the MkII might be found for a bit less on eBay than the prior SE, having nothing to do with content changes. Competing with and sometimes sourcing from Chinese firms in my own business illustrates that point often. If anyone feels wary of the MkII, default to the excellent SE and worry no further.
You're right, DIY improvements are highly feasible.
Phil