>> A population is, by definition, just an extended family
The "extended" part is the differentiating factor. You can consider that bacteria outside your ear a distant cousin. This doesn't add to the discussion.
> The likelihood that one genetically distinct population would have the same intelligence as another is basically zero
You're getting into choppy waters because "intelligence" isn't properly defined. You may find that one population's deficiency is offset by its strength in another category. Then you'd be tasked with "weighing" the importance of both in order to come up with a very subjective winner in the intelligence race. Real science doesn't work this way. This is one of the many reasons it's inappropriate to say some human population is less or more "intelligent" than another.
>> You would need a huge amount of proof and a theoretical model of why it would be the same for there to be a scientific reason to believe that it might be
The burden of proof is on the person making a claim. I'm not saying all populations have exactly identical intelligence. I'm saying that there is no reason to say there is no reason to say there is a significant difference in intelligence across worldwide populations. The lack of evidence to support such claims (and not adherence to political correctness) is the reason researchers repel such statements.
> As left alone there would be huge amount of drift and change in even just 1,000 years
No. Allele frequencies change slowly over time. Haplotype structure changes more rapidly, but even after 10,000 years you'll see general agreement of haplotype block structure within the same population.
> traveled to the himalayas and started farming goats and mountain climbing, or another group that broke off, developed writing, and for the last 5,000 years has been living in huge dense colonies and working in factories. There is almost nothing at all similar between these three environments
I don't understand what your point is here. Different populations lived in different environments, that is true. Positive selection has had time to select for desirable traits in each environment, but what makes you think intelligence wasn't selected for in all of these environments? What you are saying may some day be proven to be true, but so far there is no reason to believe that there is any difference in intelligence across different worldwide populations. There is no data. There is no proof. Your deeply flawed thought experiment does not a proof make.