Christopher hit the nail on the head with the two things that determine TH (throat hit / harshness).
Since you're sure they are the same Nicotine strength and same PG/VG ratio's... the only other factor is the flavorings.
Fruity juices (like your watermelon) tend to be a little more harsh, and bakery flavors tend to be a little more smooth... usually due to vanilla or custards in them. When I vape bakery flavors, I tend to turn up my wattage just a bit because they have a lot of vanilla in them, and that requires more heat/power, more-so than my fruity flavors... Fruity flavors do require less power/heat... This is "normal", so I'm guessing this may be exactly what you're experiencing?