There are pros and cons. The biggest advantage is that the metatarsal pad is built directly into the insole, so you'll never need to worry about a metatarsal pad adhesive loosening over time which would cause your metatarsal pad to move. Because the met pad is built directly into the insole, you'll also not feel the "edges" of the met pad that you might experience if you added a separate metatarsal pad to an existing insole.
On the other hand, because the met pad is built into a metatarsal insole, the position of the metatarsal pad cannot be moved at all. If you're looking for a very specific placement of a met pad under your foot, purchasing a separate metatarsal pad and adding into to a standard insole without a built-in metatarsal pad might be the best option.