Yes as you can see, the seats are a bit "fatter" and "flatter" then stock but only where your butt sits and not where your legs are. My husky seat is the same. So standing you won't notice. Sitting, you would notice. If your standing all the time then what ever seat you use won't matter. If you "cruise" more and like to sit then a seat like this is much better since its not up your butt crack. However if you like to bounce back from standing and sitting, then I could see an advantage to a taller seat. In the end we all like the "stock" look but want anything that is softer then the brick the stock seats are made out of.
As I see it, drilling holes in your foam is one way of trying it. If it works, great, if not you live with it till you find something else. I don't see you have anything to loose. it's not that hard to remove staples and re install, so long as you have a good staple gun.
I had the guts foam at first for my husky and I made the mistake of getting the soft foam and ended up sitting on the seat pan so it felt anyways. Most of the medium after market foams are typically softer then the stock foam that yamaha / honda and other use. Just make sure what ever brand you buy, that you get enough info before hand as to the hardness of the foam that you make a wise choice or that the company offers something like an exchange.