The kit has been optimized for using HCl to both lyse and dilute your standards and samples while used in conjunction with the neutralization reagent. If you lyse in a different buffer and then dilute with the HCl, the pH of the reaction will not be the same (i.e. the molar concentration of the neutralization reagent that was designed to neutralize the HCl may not be correct any more if another buffer is introduced into the system). Therefore, for optimal results, it is suggested to use HCl for lysis and dilution.