When it says "unless otherwise noted, a device can only have one modification" what it's referring to is Add a Matrix Attribute specifically. It's the only one that says "The Increase a Matrix Attribute modification can later be added to this modification."
Since none of the others have a clause in their description allowing for stacking, then they can only be applied once.
Which means you could take a standard issue Commlink, add Sleaze 1, then increase to Sleaze 2, and that's it. No further modifications.
Or in this case, you could modify a single point from somewhere, to the Firewall, and that's it. Firewall +1, some other -1, done. At best you can get your Paladin 9 + Pi-Tac 6 + Modify 1 = Firewall 16. Until you start loading up software.