Why could a fish not retain bacteria from the wild? Captive fish are not bacteria-free. Wood-eating plecos which have lost their gut flora tend to starve to death - as actually do many types not proven to be wood-eaters.
Puffers vary widely in their toxin levels seasonally in the wild, and also from species to species. I know of no study of their toxin maintenance or loss in captivity.
Poison dart frogs have been studied in captivity and do tend to show decreases in toxicity with time, which is doubtless dietary. Whether from lack of the proper intake source or proper precursors or long term loss of specific microflora is undetermined. I would expect puffers to follow a similar pattern, but poison dart frogs can be studied through several generations, puffers have not been so studied. The dwarfs are the first puffer to be reliably bred in captivity, and we are not yet stocked with captive-bred fish even there.
Saxitoxin is associated with FW puffers. That does not say that tetrodotoxin is not present or never present. Nor does it mean all FW puffers have that and no other toxin. Jumping to conclusions about toxins is not wise.