Correct, none of the other extensions should be affected.
This is how I check to make sure it has read the options file correctly.
1. Create a text file in this location :C:\Program Files (x86)\ArcGIS\License10.4\bin (as an Administrator)
2. Name it ARCGIS.opt
3. Add your reservation and save the file.
4. Launch the License Server Admin
5. Under Start/Stop License Service- Reread the licenses
6. Under Diagnostics > Perform Status Inquiry
You should see the reservation for Network Analyst. My example is for ArcGIS Pro Network Analyst, but you get the idea. You can see that the Pro Advanced is not affected. If you try to enable Network Analyst as another user, it will say that no licenses are available.