Ok, looking at just one system with one planet for the moment, you'll need to set a bit in the OnDominate field of the planet, call it bxxx. Then you'll need to add !bxxx to the Visibility field of the system, and create a new system which is identical to the first, only the government is "Dominated" or whatever, and place bxxx in the Visibility field. Note that the planet in the new system needs to have the "Start off dominated" flag set.
Now, to expand this to the whole Nova universe, you'll need a unique bit for each planet and station, and a new s˙st resource to correspond to each planet and station. Note that the bit structure gets really complicated for four-planet systems, since to take in to account the different order that players dominate planets, you require some sixteen resources. Another catch is that random missions would no longer work, since Nova requires a destination that will not be changed by a mission bit. Also, this may or may not work in PC Nova 1.0.6 - it tends to have a fit if the Nxxx operator is used while the player is in flight, but I don't know what would happen if the visibility of a system changed while the player was in flight...
In my opinion, it's just not worth the effort.