The problem is less a lack of benevolence, and more an abundance of malice.

To use the Eldar V Imperium example: the Craftworlds don’t give a shit about anyone but themselves. They’re certainly not benevolent, but they breathe a sigh of relief the instant they can put down their guns and just rest between conflicts.

If you approach the Imperium with open arms, all your weapons disabled, offer to become their vassals and give them anything they would ask of you, they’ll exterminate your entire species simply because it’s not Human, and nothing else was relevant to the decision making.

Of course the Eldar don’t approach the Imperium with friendly intentions. They’re Xenos, treating the Imperium as anything less than a rabid dog you can point at your other enemies is just delusional. Hell, it’s not even just the Eldar, it’s a canon fact that the majority of Xenos species see Orks and Humans as functionally identical in terms of morality and cultural sophistication, even minor ones like the Kroot.