Question about sides

So, I have my profile cutout and I am ready to take the sides down to cut the doors and the 3/8 inch cut for the hatch. I have 3/8" plywood and am planning a frame wall. Should I still make this cut per the Generic Benroy Instructions?
I am assuming that this is to allow space for the hatch seal. Is that a correct assumption?
I have a friend who is constantly telling me not to think on my own. So I am looking to those of you who have been there before for help.
Thanks

I am assuming that this is to allow space for the hatch seal. Is that a correct assumption?
I have a friend who is constantly telling me not to think on my own. So I am looking to those of you who have been there before for help.
Thanks