It is a well documented and long-standing finding that body shape varies considerably from location to location (i.e. it is not just between neighbouring pastoralist and agrarian populations but that finding is very important). The reasons for this are many and inter-related. Body shape varies with climate with sitting to standing height ratio (SSR) tending to be lower in populations from areas with higher mean temperatures. The reason for this is believed to be thermoregulatory since SSR is strongly associated with the ratio of body surface area to mass. Altitude also tends to be associated with shorter limbs and large trunks and large chest circumferences. Both of these observations are confirmed by ecological observation and animal experimentation (e.g. random allocation of members of rat litters to experimental arms). Body shape also varies with diet. Secular changes in body shape, exhibited as increases in leg length relative to trunk length, have been reported from different parts of the world. The rapidity of these changes suggests that they are due to environmental factors such as improved nutrition and public health rather than changes in climate. Pastoralist diets (e.g.) tend to contain higher proportions of milk than agrarian diets. Milk contains energy, protein, calcium, micronutrients, and insulin-like growth factor-I (IGF-I) all of which are known to facilitate bone growth. IGF-I is associated with growth in bone length and plasma levels of IGF-I are known to increase in response to milk intake. In Japan, secular changes in body-shape, exhibited as increases in leg length relative to trunk length, occurred after the addition of milk into school feeding programs in the 1950s.
It should be noted that long-leggedness may be advantageous to pastoralists. Physical models of walking and running predict that longer legs allow faster natural walking and running speeds (i.e. the walking and running speeds requiring the minimum expenditure of energy) than shorter legs. Faster natural walking and running speeds allow larger ranges with similar energy expenditures. Afar and Somali pastoralists (e.g.) herd on foot without dogs or horses. The ability to walk long distances efficiently may facilitate access to wider grazing ranges and allow (e.g.) larger herds to be maintained. This may lead to the development of a virtuous circle in which longer legs leads to increased grazing range leading to improved livestock condition, larger herds, increased income form livestock and livestock products, and increased milk availability and intake which leads to longer legs and so-on. In such a virtuous circle, "momentum" could be checked by exogenous factors such as drought, livestock disease, and competition for grazing land or endogenous factors limiting limb length. Many pastoralists practice polygyny and the association between wealth and child survival predicted by such a virtuous circle may bestow a considerable reproductive advantage upon long-legged individuals. It should also be noted that short-leggedness may be advantageous to mountain dwellers. Physical models of climbing predict lower energy expenditure and greater load-carrying capacity (due to a mix of lower energy requirements and physically lower centres of gravity of the body and the carried load). In such populations, large trunks bring the advantage of ectothermic homeothermy (Allen's rule and Bergmann's rule) and large chests with large lungs and hearts make the best of reduced oxygen environments (Hesse's Rule).
None of the above is at all controversial. It is well-established biology (Allen's Rule, Bergmann's Rule, Hesse's rule). Given this, the WHO (2006) assertion that "children the world over grow similarly when their health and care needs are met" proposed as a justification for the new growth standards is questionable.
All of this would not be of much interest to us if we did not use measures of weight-for-height (W/H) as proxies of nutritional status. Using W/H makes us see famines where there are none (low SSR = low W/H or low BMI) and obesity epidemics where there are none (short limbs and big chests = high W/H or high BMI). It makes us deny care to young children with severe wasting while lavishing care on healthier older children.
It is sensible to use W/H if we either correct the measurement for body shape (this would require weight, standing height, sitting height, and (probably) chest circumference) or if we use locally derived standards. Given the finding alluded to in the question (i.e. neighbouring groups having very different body shapes) these local standards would probably need to be very local (e.g. we would probably need several local standards in Ethiopia). Local standards are expensive and time-consuming to produce. Since we do not correct W/H and we do not often have appropriate local standards we must accept that the use of W/H in our work is inappropriate.
Regarding SSR in younger children ... There is information on this and it follows the same pattern as the data in older children (all the same biological rules apply). Here is a summary of the data that I have seen:

You can see the differences in SSR are there very early on and are persistent.
The data I used for this plot are taken from:
Eveleth PB, Tanner JM. 1990. Worldwide Variation in Human Growth (2nd Ed.). Cambridge: Cambridge University Press.
Zhang X. 1977. Studies on the physical development of children and adolescents in New China. Chinese medical Journal 3(6):364-72.
Zhang X, Huang Z. 1988. The second national growth and development survey of children in China, 1985: Children 0-7 years. Annals of Human Biology 15(4):289-305.
Eiben OG, Pantó E. 1986. The Hungarian National Growth Standards. Anthrop Közl 30:1-40.
Gerver WJM. 1988. Measurement of the Body Proportions in Children. The Oosterwolde Study. Lordgraf: Drukkerij Groenavelt BV.
Waaler PE. 1983. Anthropometric studies in Norwegian children. Acta Paediatr. Scand 308(S):1-41.
Hernandez M, Castellet J, Garcia M, Narvaiza JL, Rincon JM, Ruiz I, Sanchez E, Sobradillo B, Zurimendi A. 1985. Curvas de Crecimiento. Madrid: Editorial Garsi.
Karlberg P, Taranger J, Engstrom I, Lichenstein H, Svennberg-Redegren I. 1976. The Somatic Development of Children in a Swedish Urban Community. Göteborg: University of Göteborg & Karolinska Institute.
Prader A, Budliger H. 1977. Body measurements, growth velocity and bone age in healthy children up to 12 years of age (longitudinal growth study, Zurich). Helv Paediatr Acta 37(S):1-44.
Faulhaber J. 1976. Investigación Longitudinal del Crecimiento 26. Cordoba: Instituto Nacional de Anthropologia e Historia, Colleción Cientifica, Anthropologia Fisica.
Martorell R, Malina RM, Castillo RO, Mendoza FS, Pawson IG. 1988. Body proportions in three ethnic groups: Children and youths 2 - 17 years in NHANES II and NHANES, Hum Biol 60(2):205-22
In my own work I have used the 24-59 month group because this simplified measurements in the field (sitting height is a little tricky).
In summary:
* SSR varies over both small and wide areas.
* This variation is due to a combination of environmental and genetic factors.
* The same variation has been observed in animal models and ecological studies.
* The variation is present early in life and is persistent.
* Children the world over do not grow similarly when their health and care needs are met.
* SRR effects W/H measures rendering simplistic use of W/H universally inappropriate.
I hope this helps.