It is just a restriction on the flagship's wormhole.
Here's the full text of the card:
This ship generates a "D" wormhole in the system where it lies. When the ship moves, the "D" wormhole moves to the ship's destination system (the system in which the ship ends its movement)
When the ship is destroyed, the “D” wormhole it generates disappears
This ship may not use the “D” wormhole it generates
(Note: No other factions may travel through the “D” wormhole, not even with the Light/Wave Deflector technology)
And the rules on the D wormhole in general:
The Ghosts of Creuss have two separate Home Systems
connected by a “D” Wormhole. Both of these systems are
considered Home Systems for the purpose of card and game
effects. During setup, the Ghosts of Creuss player only places
the hexagonal tile in the galaxy. He places the non-hexagonal
tile in front of him. Also, the “D” Wormhole is considered a
Wormhole for the purposes of card and game effects.
The text in question is part of a parenthetical on the card, meaning that it's not an ability in it's own right but rather a clarification the other abilities. As a result, I think it's reasonable to conclude that "No other factions may travel through the D worhmole" refers specifically to the D wormhole generated by the flagship and not to the other D wormholes on the board (the one on Creuss and on Creuss gate).
The card would be clearer if it said "No other faction may travel through the D wormhole it generates".