I sometimes hear that Old Warhammer was satirical, and a lot of its things was them making fun of a particular group and maybe there is a message behind all the 'funny' jokes and comedic jabs.
This is something that I've seen mentioned before, often in relation to warhammer or other British stuff from the 80s and 90s, and it's something that is... true, technically, but also loses a lot of nuance and context. So I'm going to take a moment to talk about it, because I like nerding out about this sort of thing.
So! Warhammer, along with a lot of other material from the period such as Judge Dredd etc, was definitely made to be satirical. The issue is that British Satire is a strain of humour that leans very heavily on gallows humour and bleak amusement rather than more conventional comedy, which is a detail often lost when we talk about it in a wider context. If anything it overlaps with British Horror more than comedy, which itself is kind of centred around feelings of apathy and despair rather than sheer terror - whereas an American slasher fic might focus the horror on the unstoppable murderous serial killer chasing you, the British horror will be when you scream for help and the people in the house nearby just roll over in bed or turn up the volume on their TV. It's a satirical depiction of the general indifference of our society to the life and happiness of others, and how incredibly easy it is to fall through the cracks or be failed by the institutions that should be there for you, rather than "making fun" in the way its normally understood.
Warhammer Fantasy, then, was
extremely satirical, especially in the early days. The land is ruled by aristocrats with curled wigs and perfumed hair and triple-barrelled names who are all comedically incompetent and self-absorbed... and if you disrespect them, you'll get tortured to death. The Ulricans use throwing up the horns as a holy symbol and the Sigmarites chant about how they need a piss in not!latin because they don't understand the dwarvish words in their prayer books... and if you were born looking wrong, they'll burn you at the stake. The vile ratmen lurk beneath every street and building, eating babies and spreading plague and pestilence... and if you go to the authorities for help, they'll have you committed to an asylum rather than admit there could be a problem.
There's often an assumption, when people say "oh it was meant to be satirical", that this means you shouldn't take it seriously, its just a joke, lighten up. But Warhammer is a British product born out of the Thatcherite years and all their misery and inequality, and when it uses satire, it isn't meant to be light-hearted in the slightest.
Now don't get me wrong, the Crusades as presented in the game are still kinda shit, largely because of the issues you mentioned wrt just treating the natives as accessories or props in the story of the Crusaders, not caring about them as people in their own right (and also being hella racist). The satire is found in all the peripheral stuff that the authors did care about - the adventuring lords who decided to go tomb robbing and got murdered by grumpy Nehekharans, the Knights Panther who were so obsessed with their new status symbol they hunted the big cats to near-extinction, the Estalians who embraced this grand unifying moment against an external foe and then promptly fell apart into bickering and strife a few years later.
The Knights of Magritta are a 2e organisation, for example, that highlights this - they're a secret society spread throughout the Old World whose founding purpose in the aftermath of the Crusades was to agitate for finishing the job, conquering the land entirely as the only way to protect the land's "soft southern underbelly" from the Arabyan scourge. They're an old relic by this point, cut adrift and struggling to find their new path forwards, because as it turns out friendly diplomacy, trade ties and cultural exchange did more for protecting the Old World from Araby than a hundred Crusades could ever hope to manage. So now the Knights are nominally opposed to Araby and Arabyan influence wherever they can find it, but none of the leaders actually believe in or want a new crusade any more, they just want to keep agitating against the perfidious arab as a way to line their own pockets and maintain relevance in a world that has left them behind.