And if there’s no real difference between them, why have different species of humanoid in the first place
One way to give them that real difference would be to distinguish them by geography. I could envision a campaign where, say, there are humanoids all over the place, but where you go determines what sort of humanoids you find. This could be done in the Flanaess; the hobgoblins of the Great Kingdom, the orcs of Iuz and the Bandit Kingdoms, goblins as the scourge of the Sheldomar Valley, etc. That would give some nice flavor in terms of distinguishing one area from another, as well as providing for a means of tipping off players that something’s Not Quite Right (“Those were kobolds! There shouldn’t be a kobold within a thousand miles of here
Another way to regionalize your humanoids is to give them some real distinguishing characteristics or abilities that differ by geography. If you just have to have your orcs and goblins shuolder-to-shoulder across the land, you can still break things up and give the players an unexpected twist. Perhaps the orcs in the northern Vesve Forest have honed their archery skills out of necessity from combatting the nearby elves, and now have a +1 to hit with the longbow (which is carried by 75% of them in addition to their regular weapons). The hobgoblins of the Bone March, on the other hand, might have mastered the giant lizards of the region, and formed a force of cavalry mounted on the beasts. Perhaps the goblins of the Pomarj are chaotic evil rather than lawful, and their behavior and tactics will be changed as a result. The kobolds of the Hollow Highlands could get a +1 to hit with their trademark blow guns.
Humanoids don’t have to be as cookie-cutter as they are in many games, or as uniform as they are presented in the Monster Manual. On the other hand, their modifications shouldn’t be capricious (well, *these* gnolls are blue, and they have 8 HD each!). Assigning the characteristics by region helps with both of these goals.