[My emphasis]
I will note that you said “is widespread in India” NOT “was in India” – the paper is about modern populations not ancient – and my question is about ancient populations.
[Addendum: on closer examination, that paper does not even cover the Indus Valley, which is in modern-day Pakistan, and the paper only covers states within modern-day India – making it even more irrelevant!]
Given that populations move, and genes spread, over the millennia, it is the genetic makeup of the ancient Indus that matters, not modern India.
As we have no evidence that R-M124 is basal in the ancient Israelite population, and a whole heap of evidence (which you have failed to address) that it isn’t, R-M124 would appear to be completely irrelevant!
As I said before:
[Addendum:
But I have in fact found an answer to your irrelevant question:
The question remains of how distinctive is the history of L1 relative to some or all of R1a1 and R2 representatives. This uncertainty neutralizes previous conclusions that the intrusion of HGs R1a1 and R2 from the northwest in Dravidian-speaking southern tribes is attributable to a single recent event. Rather, these HGs contain considerable demographic complexity, as implied by their high haplotype diversity. Specifically, they could have actually arrived in southern India from a southwestern Asian source region multiple times, with some episodes considerably earlier than others. [1]
So it seems that R-M124 came to India from southwest Asia.]
Easy:
The Kassites and the Phoenicians met the Late Harappans in Bahrain.
There’s an explanation in that very paper.
Though I’m not sure that this is even relevant, given that the evidence seems to be that the Paleo-Hebrew alphabet derives from the Phoenician alphabet which in turn derives from the Proto-Sinaitic alphabet, which are all native to the area.
But I would note that writing systems are far more portable than language. We speak a Germanic language, yet use Romano-Greek script and Arabic-derived numerals. A number of countries have changed writing system even in the last century.
This quibble still does not address my original point:
Please explain why you have not addressed my explanation WHY “Indus is completely awful!”
Given that the oldest *proto-*Hebrew writings date back only to the 11th-10th Centuries BCE, this is a ludicrously silly request. The Bible itself isn’t that old.
Because “Mizraim” is a Hebrew word, not an Egyptian word!
Please reread this:
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Please demonstrate how what word Arabic used for Egypt “< 1300 BCE” is relevant.
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I rather doubt we have any surviving Arabic writings this old.
Hell no!
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Your claim was “No character parallel to Moses in Egyptian literature” NOT “No character parallel to Moses in Egyptian literature before 1500 BCE” – you are attempting to move the goalposts here.
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There is no evidence that Moses himself existed in Hebrew literature that far back.
So this issue, as with nearly every other issue you have raised, is utterly irrelevant!
I’ll do so after you explain all the parallels between all the gods and heroes in all the world’s myths and legends. 
Trying to cherry-pick a single set of parallels out of that vast number, and declaring that only they are meaningful and worthy of explanation is a a fallacious Special Pleading.