No, if the higher IV-IV character will be able to receive the same stat bonuses from merging, thus, two characters that have merged the maximum number of times (10) will have the same bonuses, with the betterhigher-IV character having the same advantage as before. This is explained in this thread:
You can merge up to a maximum of "+10". At Lv40, each merge gives 2 stat points. At "+10", you always end up with 4 extra points in each of the 5 stats.