That is more to do with extract_f2. When you generate f2 stats there are two major settings to consider, maxmiss and afprod.
Maxmiss=0 uses only the snps covered by all populations that you are generating F2 for. Note that if you generate F2 for a bunch of pops, and you decide only to use a subset of them in your test, you still only get the snps that were covered in the total bunch. That being said, maxmiss=0 is probably most suited for 'rotating' qpadm, or qpgraph, where you are going to be using the same populations for a large number of trials. I haven't played around with afprod settings much with maxmiss=0, but I think generally the default is afprod=false.
Maxmiss=1 is like setting allsnps=TRUE. For whatever reason, maxmiss=1 + afprod=false is a big-nono. The results in many cases are fine, but there are some that flat out contradict direct from genotype data. If maxmiss=1 then must afprod=TRUE.
The results from precomputed F2 do vary slightly from direct from geno, but it's not anything too crazy. Here was a test I did in 2021 when first started using admixtools2.
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Spoiler
F4 FROM GENOTYPE DATA
South_Africa_2000BP.SG GoyetQ116_1 Tianyuan_AR33K Onge.DG -1.465
South_Africa_2000BP.SG GoyetQ116_1 Tianyuan_AR33K Ust_Ishim.DG -0.4846
South_Africa_2000BP.SG GoyetQ116_1 Onge.DG Ust_Ishim.DG 0.722
South_Africa_2000BP.SG Tianyuan_AR33K GoyetQ116_1 Ust_Ishim.DG -2.587
South_Africa_2000BP.SG Onge.DG GoyetQ116_1 Ust_Ishim.DG -0.01835
South_Africa_2000BP.SG Ust_Ishim.DG GoyetQ116_1 Tianyuan_AR33K -1.984
South_Africa_2000BP.SG Ust_Ishim.DG GoyetQ116_1 Onge.DG -0.7228
F4 via f2_from_precomp (maxmiss = 1, AFPROD = TRUE)
South_Africa_2000BP.SG GoyetQ116_1 Tianyuan_AR33K Onge.DG -1.26
South_Africa_2000BP.SG GoyetQ116_1 Tianyuan_AR33K Ust_Ishim.DG 0.01
South_Africa_2000BP.SG GoyetQ116_1 Onge.DG Ust_Ishim.DG 1.00
South_Africa_2000BP.SG Tianyuan_AR33K GoyetQ116_1 Ust_Ishim.DG -0.77
South_Africa_2000BP.SG Onge.DG GoyetQ116_1 Ust_Ishim.DG 0.91
South_Africa_2000BP.SG Ust_Ishim.DG GoyetQ116_1 Tianyuan_AR33K -0.75
South_Africa_2000BP.SG Ust_Ishim.DG GoyetQ116_1 Onge.DG -0.16
I don't remember how to get gendstats, details=YES sounds right.