I also read it as 'younger' (see post title), but what they meant by younger and youngest in the early 1700s is anyone's guess.
He had two daughters named Mary, one by each wife, who both were still alive in 1703, and are both mentioned in the will.
Mary daughter of the first wife was about 20 years old when her half-sister Mary was born.
I have seen that happen in other families as well. They seem to have figured that since the older child was an adult (or nearly) then the name could be recycled and used for children of the second wife.
I have also seen Mary Ann and Maria in the same family (and same mother), Elizabeth and ELiza, and so on — and all survived to adulthood and married, etc.