You can set your own rules for LOOT. I find that I have to manually re-sort a little more with it than I did with BOSS.
That shadowing is weird. Do you see it in different circumstances (buildings, women, elves, whatever), or just on faces and arms?
One thing that popped into my head was ENB and specifically any DoF, sharpening or grain shaders that you're using. Some shaders apply a pattern to a map and overlay the image. Or a combination of a low quality setting or low sample size with a certain shader might result in that.
If it's only happening on skin, I'd look at the [SUBSURFACESCATTERING] section toward the end of enbseries.ini. Maybe also at SSAO.
You could temporarily improve the quality and sample size options to see if it fixes that, at the cost of performance. Make a backup so you can revert later.
In [SSAO_SSIL]:
SamplingQuailty=0
...
SizeScale=1.0
SourceTexturesScale=1.0
FilterQuality=0
In [SUBSURFACESCATTERING]:
Quality=0
In general, for Quality settings, -1 is max quality and 1 or 2 is min quality, max performance - usual settings are 0 or 1.
For SizeScale and SourceTexturesScale, 1.0 is high quality, 0.5 is medium quality/performance - usually set between 0.5 - 0.75.
For grain, DoF, etc,. you can temporarily turn those off in the ENB Gui, or by setting the variables to 'false' in enbeffect.fx.ini.