The Warhammer fluff is a background for their tabletop games. Nice, good fun, but hardly 'realistic' (We are obviously talking about fantasy here). It forms a good basis for further thought, but that thought is needed if you wish to translate it into roleplay background that stand the test of critical thinking.
Let's take a planetary assault. If we follow the fluff, this might start like the Battlefleet Gothic Example of the same name, in which the invading fleet has to run the gauntlet to get enough attackers on the planet. This makes for an entertaining game and seems to lock in seamlessly with the description from Codex Planetstrike, but it is utter and complete nonsense.
For no sane commander will hazard his invasion forces before he has driven of the hostile fleet. This applies not just to modern military history, but to all military history as we know it. Take the Falkland Islands campaign as an example: the British Navy first chased the Argentine Navy to port and only then brought in its landing forces. The same pattern that applied to all operations in the Pacific. Or to earlier ages. Only if time is of supreme essence should a direct attack in the face of a hostile fleet be considered. This could happen. But should hardly be the school solution. The Tactica Imperialis solution can only be: gain system supremacy through fleet action (your BFG scenario minus the transports), reduce planetary defenses as far as possible (which is a risky business) and only then bring in your invasion forces.
The same applies to attacking in the teeth of the defenses. Again, it makes for a cracking game and paints a great picture,but makes little sense. The closest real world example that spring to mind is a parachute assault and there is a reason parachute forces have declined since WW II: against determined opposition, they stand little chance. Air defenses will savage them and once on the ground they are horrendously vulnerable against heavy forces. There might be cases where such a direct attack is the only option. But they should be rare indeed. There is a good reason any naval or airborne invasion I know off aimed for a weak point in the hostile defenses and tried to get a good hold first. Only if you have to get down right now should a direct assault be executed.
For in a real total war there are no such things as critical victories that win a campaign in a few hours, unless perhaps you are defending against an invasion and manage to destroy the enemy during its initial attack. Knocking out a command center or a vital industrial complex can indeed be decisive in the long run, but only because it gives you a crucial advantage in the following battles against the enemy main forces.
And pacification is the next chapter. We have seen in Afghanistan and Iraq that getting in can be deceptively easy, especially against weak opposition. But getting the whole area under control is a different ballgame.