I know that 5 necron ships travelled to Mars... only one reached the surface and it was destroyed quickly, as you said.
Anyway, I guess you're right about Dawn of War's lore... yes, a book has been written about it (well, actually, if I'm not wrong, the game is based on the book) but that's just for the campaign background... besides from balance, I got a bit annoyed in Dark Crusade and Soulstorm when I saw Space Marines, Imperial Guard and Battle Sisters fighting each other...
I also didn't like their intros... the one with those 2 space marines charging the monolith is just weird DX.
Also, like I said before, units have been badly modified: for example, Necron immortals are not just an anti-tank unit... one squad can kill loads of infantry or succesfully hit a vehicle more than once.
I have a little question related to the TT game: is it true that Games Workshop will remove the Imperial Guard's Doctrines system? I read that on the Wikipedia as a rumor some time ago... my little army is based on them and, also, it would be a shame to remove such a customization system.