Well, think about how waypoints work for us? First, you need to walk right up to them to get them added to your list. The enemy armies would have to walk into Cyseal, which is home to its own army.
Since they have several NPCs working for them i think that can be easily arranged.
But, this is not a serious complaint really. Im aware this setting has several features that require some measure of "turning a blind eye" from the more discerning players, as any high fantasy does.
On the other hand...
If anyone would actually want a internally consistent excuse for this:
"Arhu controls the waypoints and he has sealed them from entry by anyone he doesnt want to have access to them. That includes all residents of cysael city since ha cannot be sure who is the hidden malefactor or is there more of them - even in ranks of the legion. Legion tried to use waypoinst closer to the city in the beginning, but all who went through them were quickly annihilated by the undead forces.
When Source hunter he called in to investigate came in and decided to lend a hand against the undead threat, he decided to attune the waypoints to them alone, since he could rust them and to enable them to swiftly move around."
all this needs is a bit of a text adjustments during the beginning. Somewhere.
maybe in the dialogue at the gates.