Except that orcs are usually portrayed as invaders, not as indigenous peoples defending their lands. If anything it's the human(or other) settlers who are presumably the ones indigenous to whatever area orcs choose to occupy.
I don't see that.
The Keep on the Borderlands is explicitly a small fortified town in an area dominated by humanoid settlements (including orcs). The implication is the humanoids are the natives, while the humans are trying to tame the area for civilization. Which makes humans the invaders.
In the Forgotten Realms, the North is explicitly called the "savage frontier". Vast areas are dominated by humanoids, while the occasional human settlements are points of light in the dark. While the time scales are wonky (aren't they always, in fantasy worlds?), it's also clear the humans are relatively new. Sure, the humanoids form into hordes and periodically descent upon civilization, but even the hordes tend to attack the incursive human settlements like Silverymoon or Waterdeep, rather than more established humans areas like Tethyr. So again, humans are the invaders.
It also fits the general Western ethos of D&D in general.
I'm not really familiar with Keep on the Borderlands (I don't generally play modules), though, I suppose that's a plausible scenario, given that humanoids must dominate
some territories if they exist in the world. But that's hardly the only type of scenario there is and it's also not always a clear cut case of certain territories being exclusively humanoid or human and whatever species is attacking at any given time being a non-indigenous invader.
In the case of Forgotten Realms for example, the "savage frontier" is actually full of human barbarian tribes IIRC, such as the one where Wulfgar (one of Drizzt's friends from the Icewind Dale trilogy) comes from, as well as dwarven settlements. It isn't
just orcs and other humanoids that live there, and they hardly occupy the entire area. Many areas are just unsettled contested territories with few arable land, where humanoids may sometimes descend upon from farther away mountains where they actually live.
Also, my impression of humans being relative new in most fantasy settings is usually in relation to elves and dwarves, which are usually portrayed as being the older races that already occupied the lands before humans became numerous and prosperous and started expanding into their territories. Which is usually part of the reason given for elves being so aggressively protective of their forests, and would also be an example of an "indigenous" race that's not portrayed as vermin, but if anything as being superior to humans, but less numerous.
Waterdeep itself is build on the site of an ancient elven settlement according to the
FR wiki (though, it doesn't go into specifics on what happen to that settlement, if it fell to invasion or what), and started out as a trading post between (presumable human) northern tribesmen and southern merchants. It's hardly the site of human conquest of humanoid lands.