They're definitely different. The latter case evaluates not X in a boolean context first and then checks to see if the two objects are the same object (either True or False).
Consider:
False is not []
This expression is trivially True since False and [] are quite clearly different objects. 1
vs.
False is (not [])
This expression is False since not [] evalutes to True and False and True are different objects.
Of course, this is just one example. It gets even easier to find examples if you don't use False and True explicitly as the second expression will always be False and the first expression will (almost) always be True...
3 is not 0 # True
3 is (not 0) # False
1Note that is not is a single operator in the same vein as not in.