The Daleks fighting someone in Earth Orbit worried the Torchwood Empire enough to delay their plans for war with Starfleet Command until they know if they are being invaded.

The Human Interstellar Civil War was something the Time Lords now wanted changed when the Daleks got caught in the middle of changing history because of it on their watch of the whole thing happening.

The Starfleet Imperium had colonized several planets without the knowledge of the Torchwood Empire for Building Boot Camps to "Train Starfleet Marines to defend Humanity from the Torchwood Xenophobia making enemies from other species!" and protecting Earth Cargo Ships from being attacked on Trade Routes at the same time.

The first surprise the Ninth Doctors both had was the Starfleet Imperium being a military dictatorship run by Emperor Zefram Cochrane's Clone and the Time Lords approved the whole thing to develop weapons against the Daleks.