Not sure if this was intended as designed, or GGG just accepted it as a consequence of the shaper guardian maps being differently designed (i.e. - being their own map rather than an implicit modifier of a standard map).

In any case it seems weird that they are the only maps that you own (as opposed to kirac missions, which make sense to not be affected by your atlas passives since they happen on kirac's atlas and not yours) which are not affected by your atlas passives.