The first thing I said when I ran a Rogue Trader campaign: "The Warhammer 40k universe is a big place and you can find tons of information about the setting. Some of that information contradicts itself, and like I said, it's a big place, so even if the lore is applicable in that part of the galaxy it doesn't go to follow that it's applicable in this part. If something in this campaign doesn't match the lore as you understand it, just roll with it and accept that it's different in this part of the galaxy."
I'm one of those people who likes lore. Er, when I like the lore. But the primary purpose of lore for a game is to serve the needs of the participants. It's nice that I can play a Star Wars game and we're all pretty much on the same page. I don't have to explain what the Empire is all about, who the guys in white armor are, or what a Tie-Fighter is, I can just hit the ground running.
I'm not one of those people who demands fidelity right down to the smallest detail, but if I'm invested in a setting, big changes will leave me unhappy. If I sit down to play a Star Wars game with you, and you tell me the Force is caused my some sort of bacteria that lives inside you, and the more of this bacteria you have the stronger in the Force you are, it's just going to piss me off. But I'm not going to give a damn if you tell me Commander Jord is the Moff of Omicron Persei VIII when in setting it's actually Lrrr.
Star Wars is probably a bad example given it's ubiquity in popular culture. For most games, the sad truth is that most players don't really care all that much. A lot of GMs might care, but players? Not so much.