No, you'd still use the perma-proto breakout to access the GPIO you need, but using a header with extra tall pins allows you to stack a HAT on the top of your IR circuit if you wanted to at a later point.
... That's just a suggestion though, since you have a choice of which header to solder to the perma-proto. Soldering the header that comes with it will be slightly easier, but this will give you room to expand.