The reason water municipals are switching from Chlorine to Chlorine dioxide is because Chlorine is much more harmful.
Chlorine reacts with contaminants in the water forming carcinogens.
The second link you gave says.
after 8 wk of treatment T4 levels rebounded to above pretreatment levels, coinciding with an increase in thyroid radioiodide uptake. This T4 rebound phenomenon and increased Iodide uptake may be due to a compensatory endocrinological mechanism.