I think the problematic tropes are the savages of the jungle. This is apologism, but large chunks of the world were once vast tracts of cannibal-filled forest. It makes for exciting adventure. Even this trope isn't evil though. More neutral-hungry.
Pointing out that there is evidence that the celts practiced sacrificial cannibalism. You can avoid a lot of issues if all your cannibals aren't BIPOC.
To me the most interesting and provocative part of that article was this:
...The concept of an “evil race” becomes a cop-out. With later campaign settings like Spelljammer, Planescape and Eberron moving away from the concept.
I don't know Planescape well but what I love about Spelljammer is the opposite of this: Large Luigi aside, Spelljammer makes zero attempt to paint mind flayers, beholders, and neogi as anything but evil... but the setting is cosmopolitan enough to expect you to get along with them anyway. At least while you're in port.
A large part of Spelljammer's flavor comes from having LOTS of alien bad guys all in conflict with each other, and players getting to choose which factions they'll ally with to achieve what goals. (In Spelljammer even the Imperial Elvish Navy is usable as a bad guy faction!)
So, Eberron has this as well. There are always evil things in the universe, because extraplanar beings are incarnations of ideas like evil. You can't have a good demon because a demon embodies a particular type of evil; if a demon somehow ceases to be evil, it also ceases to be a demon, which will be accompanied by a physical transformation into the new concept that it does embody.
Races are not this way in Eberron because races are a way to explore culture. IMO, it is all well and good to explore human culture, but for many (most) players, every PC is culturally indistinguishable from the players, and every NPC is treated as culturally indistinguishable by the players (and usually the DM, if we are being honest). OTOH, players tend to buy in to differences in culture among demihumans and humanoids, partly because of the tropes associated with them, but also because they are just a bit alien by design. IME, even if you subvert a demihuman's or humanoid's tropes, players still buy into the new culture you have constructed, particularly if you build it into a known trait (like martial hobgoblins or the longevity of elves).
Also, points for quoting Brust.
So...I will now start the debate that painting ALL humanoids as evil....to me, that heavily borders on Railroad play. It reduces choices. It reduces roleplay (i.e. I just slaughter them all because they are evil). It makes faction play in Caves of Chaos obsolete depending on character class/alignment....why bother working with them, they are evil and we are good, lets slaughter them, etc.
I agree with this.
P.S. I truly do not comprehend how or why some people mentally associate pre-Warcraft orcs with real-world minority groups like Native Americans. Tolkien wrote them as industrialized fantasy Nazis, and if those cartoons diverge from that it's only to make them look more like Neanderthals or trolls ("bash 'em, smash 'em, skin 'em alive!"), not ANY kind of anatomically modern human being.
D&D orcs are swarthy (black or "brownish green " i.e. olive skinned) subhumans with overactive libidos who rape our women. Tolkein orcs were slant-eyed, flat nosed and yellow skinned. You really don't see how people connected those to existing racial tropes?
[1] I think those kinds of "special" orc challenges are actually more interesting if the species in question does have an "always evil, kill on sight" reputation.
It can still have the reputation. The reputation isn't necessarily true. Players having to figure out what is true is one of the most interesting parts of the game for me.
It is no improvement to just reverse the roles, either; genocidal humans with no redeeming characteristics, fighting noble savages who embody all that is good and pure in nature, are no more interesting. You just exchange one "always true" condition for a different "always true" condition. What I find more interesting is
uncertainty.
[2] Faction play seems orthogonal to alignment discussions, more closely related to depth vs. simplicity. You can totally still have faction play with several factions of Always Evil beholders, neogis, and mind flayers for example. What makes faction play difficult is if they are simplistically evil with no behavior other than "suddenly mind flayers attack!" But as long as the mind flayers have realistic constraints on their capabilities ("there are only 23 of us, with 400 goblin slaves") and unfulfilled goals ("we'd really like to be the ones collecting protection money, and brains, from the coastal territory nearby") you can have meaningful Diplomacy-style faction play as well as sneaky Mission Impossible-style infiltration/deception play.
You can argue that allowing some fraction of mind flayers to act like sympathetic humans theoretically enables even more kinds of faction play, and technically you'd be right (although why not just use humans in those particular roles instead of humans in rubber masks? Alien psychology should be inhuman). But faction play doesn't require it.
All true, and this is part of why I think a degree of uncertainty regarding monster intentions is interesting. Although, in my game, mind flayers are incarnations of the
fear of that which is alien, so they do to be evil because they do things that mortals fear.
[3] At the risk of repeating points #1 and #2, I see no conflict between "Always Evil" reputation or even basic psychology, and occasional helpfulness from members of that race. The sweets-addicted troll may be more than happy to help you kill a dragon in exchange for a share of the treasure. He may even deal faithfully with you instead of betraying you, especially if he's got a long-term partnership in mind. That doesn't mean he won't snack on a three-year-old toddler if/when he runs out of pastries, and if there are no consequences to him eating it.
Also true, and this is how I treat the incarnations of evil. Incarnations of evil often want to make deals or work with you; for some, trying to corrupt you is in their nature. You know they are evil, you just don't know what their true motive is, and whether (or when) it will lead to betrayal.
EDIT: BTW, the incarnation of evil ideas can be an interesting way of differentiating the personalities and motivations of demons, devils and the like. If you make a demon represent the fear of a particular type of thing, like fire or insects or filth, that can modify how it looks, how it behaves, what it's lair looks like; all should be calculated to creep out or terrorize the players out in a particular way. Likewise, if your devils represent a particular type of corruption, their look, motivation, behaviour and environment will be designed to try to corrupt players in that particular way.