SNS-HDR is not an HDR creator, but a tonemapper (granted though, the best for that purpose). The Neutral preset just gives the exposure blended result that's assembled from the individual exposures, before any tonemapping but after exposure fusion/merging.
I now worked tested some more, I guess it is more about me being a beginner in HDR than stuff is not working. I stitched each exposure separately to 16 bit tiff in Hugin, 3 layers 2 stop separated, and then made a neutral tone-mapping in SNS-HDR and saved as 16 bit tiff, and then I got desired result - no clipped highlights, noise-free shadows, and a totally neutral render.
One should not be in a hurry though, it is not fast software. I had a crash too, will be interesting to see 3 x ~190 megapixel merging that 6x6 medium format will be... I now do my test on 36x24mm, sampled at about 45 megapixels.