I think the CaCO3 and MgCO3 accumulating in the medium sets you up for two issues - high pH, and upsetting the osmotic balance, therefore drawing water from the root cells, both upsetting their internal chemistry.
I don't know what impact chelation would have, as that's intended to make a relatively insoluble ion more stable while in solution, so may play little role, if any, upon the process of drying, concentrating, and precipitating.
I was thinking more along the lines of incorporating a chemical injector with a strong solution of EGTA/BAPTA, and perhaps some citric acid to balance out the pH. Would be more like a maintenance thing rather than "saving".
Hypothesis being that the salts really aren't too bad for the plants, but its rather the accumulation of the precipitates that are. By adding a chelator, you're insuring the next time you water it will be "flushed" out, rather than precipitate out.