Also interesting is this table of phenotypes across the ages in Northeast Europe. I have laid over colours to visualise the evolution more easily. Fatyanovo R1a-Z93 tribes had an overall pigmentation similar to that of modern upper-caste North Indians. If they weren't nearly as light as modern Northeast Europeans, it isn't surprising that Indo-Aryans also weren't lighter skinned or haired, even without blending with other populations along the way. It's really during the Iron Age that Northeast Europeans started becoming blue-eyed blonds. Mesolithic EHG were as dark overall as Sub-Saharan Africans (imagine them looking more Ethiopian or Somalian). Mesolithic Latvians had blue eyes, but they were admixed with WHG (Y-hg I2), while Mesolithic Russians were pure EHG (Y-hg R1a).
Mesolithic EHG as dark as Sub-Saharan Africans? Wasn't it usually established by all the prior genetic studies about EHG that they had at least some of the skin-lightening gene mutations so they probably had reasonably light skin, contrary to the WHG? Even for the WHG I tend to think they had minor depigmentation mutations just like those that cause modern Sub-Saharan Africans to have a range of distinct skin colors even when they lack any non-negligible West Eurasian ancestry. Not that I think that they were light-skinned, like those denialists that always exist usually for the wrong reasons, and not just because of scientific skepticism. I rather envision the WHG as being basically Khoisan-like or maybe Tigray/Amhara-like in skin color, that is, dark, but certainly less dark than the average Sub-Saharan African. They lived for many millennia in latitudes that are far more temperate and less exposed to strong sun radiation than anything that exists in Africa (even the Cape region), and much (most?) of their ancestry derived from even earlier Gravettians that had lived in Europe also for a very long time. I really doubt that would've caused no skin depigmentation
at all since the out of Africa migration.
As for the Fatyanovo R1a-Z93, I had already suspected that was one of the main early Indo-Iranian cultures, but are you sure about their complexion being similar to that of upper caste North Indians? Maybe those North Indians of upper caste who look lighter, but the average of them still looks pretty dark-skinned even compared to Pashtuns and Balochs, let alone to Europeans.
I think we could expect the Indo-Aryans to be at least a bit lighter-skinned than the lighter half of the upper caste Northern Indians, considering the average Yaghnobi Tajiks' (who have as much as ~40% steppe_MLBA ancestry) skin complexion, which is pretty light (though not "Northeastern European" pale skin), and also simple logic: if you mixed mostly Dravidian-like people with just a minority of Upper Caste North Indian-looking people and put them to evolve for more than 3,500 years in tropical and subtropical but not high-latitude areas (so, no strong selective pressure for skin depigmentation), you'd get people who have a darker skin complexion than the modern mixed Upper Caste North Indians have.
But, after all is said and done, I agree with you, and Razib Khan had already argued that months ago: the CWC-derived people were still mostly pretty "swarthy" in comparison with modern North Europeans, and the lightening process accelerated a lot after 4,000 years ago.