If i read thoes plans right, they do account for sub displacement. the volumes listed in the actual diagrams usually add up to more than what the plan is labled as. because of this i am going to assume that once you get a sub in the box you'll loose a little bit of internal volume bringing down the volume to what the plan is labled as.
sub displacement technically does affect the tuning of a box but its only to a point where you will not notice it. whenever you lower the NET volume by either adding a brace, piece of wood or larger sub you will raise the tuning frequency a bit. enough to be able to tell? not really. but technically yes.