I agree that they should have thought it through better. Might have something to do with the first story draft being more along the lines of a Heart of Darkness like story and the resulting loss of time and energy for the actual script.
But then again you have the same problem in most Trek stories with background stuff. WWII and the Eugenic Wars that serves as fictional historical background for so many Trek stories, from Kodos and Khan to the pilot of TNG, Bashir and the end of ENT, has always been pretty vague. But OK, in this case vague isn't a problem; there are no contradictions like in INS.
Yet in ST09 the 24th century background story makes no sense, whether you include Countdown or not. Spock wanted to help the Rommies and then Nero blames him? Shouldn't he rather blame his own government instead of the Vulcans who helps and fails? Is it Romulan upbringing (don't question the leaders) plus racism plus the desire to find a scapegoat in a catastrophe? No idea, you have to guess to make sense out of it.
But then again the movie hardly fails because of this, does it (who cares about motivations; Khan didn't really have a reason to be angry about Kirk in TWOK either, he did after all choose his exile)? And I would claim the same in the case of INS, it doesn't fail because the background about the Sona and Baku is unclear.