Tsubasa,
The communications channel formula is not dependent on how your team is structured from an organizational point of view. All the formula does is take the number of people and calculate the number of channels.
Examples:
If you have a self-directed team of 6 people, then you calculate 6*(6-1)/2.
If you have a self-directed team of 5 people & 1 project manager, then you have 6 people on your team and you calculate 6*(6-1)/2
If you have a dysfunctional team with 5 people & 1 project manager, then you have 6 people on your team and you calculate 6*(6-1)/2
If you have a self-directed team with 2 blond people & 4 people with black hair, then you have 6 people on your team and you calculate 6*(6-1)/2
So you first decide who is INCLUDED in your team, then you calculate the channels.
However, WHO is included in "N" is a totally different discussion, which is beyond the PMP exam: If you feel that the PM is indeed part of the team, then you include the PM in that number (6). If you feel that the PM is not part of the team, then leave him out (5).