I would not rule out dioxins as a another contributory cause to CKDu.
Bullet points from the article.
Prevalence 15%  affecting a total population of 400,000 patients with an estimated death toll of around 20,000
Individuals who drink treated water from large water supply schemes (especially in the twocities of Anuradhapura and Polonnaruwa), while living in the same endemic areas, do not have the disease.
Jaffna and Northern province which has very hard water (Fig 1) has low incidence of CKDu because agro chemicals were prohibited during the war.
Three potential sources of glyphosate/AMPA-metal complexes:I can well attest to the heavy usage of RoundUp out here in the Wanathavillu/Eluvamkulam area. RoundUp is used to clear paddy fields, vegetable plots, road side, gardens of weeds. Its much cheaper than using manual labor. That said as far as I know there arnt any patients suffering from CKDu. Probably attributable to drinking water wells are by the side of tanks/wewas like Ralmadu and Nelum Wewa or are diluted by Kala Oya waters. All other wells the water is absolutely hard and undrinkable.
[Glyphosate/AMPA + Ca/Mg/Fe/Sr ] complex in drinking water. [Glyphosate/AMPA + Cd/Cr/Ni/Co/Pb/Vanadium (V) or As] complex in food. [Glyphosate/AMPA coming from dermal/ respiratory route] + low amount of [metals/As] from water and foods, here the complex is formed within circulation.
Research shows that Roundup (glyphosate) and its principal breakdown product, Aminomethylphosponic acid (AMPA) is taken up and accumulated in GM soy bean.
All of the individual samples of GM-soy contained residues of both glyphosate and AMPA, on average 9.0 mg/kg. This amount is greater than is typical for many vitamins. In contrast, no sample from the conventional or the organic soybeans showed residues of these chemicals .
Jayasumana, C.; Gunatilake, S.; Senanayake, P. Glyphosate, Hard Water and Nephrotoxic Metals: Are They the Culprits Behind the Epidemic of Chronic Kidney Disease of Unknown Etiology in Sri Lanka? Int. J. Environ. Res. Public Health 2014, 11, 2125-2147.