Except their "just multiply the whole thing by a bunch as you add more" theory is really awful. It's the opposite of what you should do for monsters without synergies, especially melee-centric ones who will have difficulty bringing their might to bear and are easily taken down by AE, and the math/break points on it are silly.
On the other hand, some monsters have extraordinary synergies that could just be called out. Intellect Devourer could be double xp when grouped with a monster that incapacitates (stuns), triple xp when grouped with other intellect devourers. Now DMs won't be surprised when one intellect devourer sets up the other to automatically devour the brain of a PC. And it's not like the math is fiddlier than what we have (which is pretty awful). Hobgoblins have synergy with, well, everything, so are pretty crappy XP on their own, but great XP as soon as you add any number of melee-capable allies.
P.S. The really sad thing about the intellect devourer example is that it doesn't really get much easier as you level. It's not like your save bonus goes up much, so running into 10-20 of them at high level? Better not be surprised, win initiative, and hope you can kill almost all of them before they go.
Huh, I just don't see the encounter building guidelines that negatively. For one thing, as many have pointed out, they are just guidelines. With how many creatures there are bound to be some interesting examples of how creatures can work together, but I think that changing a creatures XP based on who it was fighting with might get unwieldy quickly.
However, I would argue that the difficulty of an encounter almost always scales up faster than linearly based on how many creatures you add regardless of which creatures are used. Enough kobolds for a moderate encounter for a higher level party will quickly get out of hand for the party. There will be so many that even a few fireballs will not take them all down, and with pack tactics, there will be plenty of 20s rolled.
As for the intellect devourer example with 10-20 creatures, it would be difficult for that group to surprise anyone. Either some of them roll low on their stealth check or someone has a ridiculous passive perception. Our rogue/monk has a passive perception of 19 at level 5. The party should realize that 15 creatures need more than a run in with guns blazing strategy. The intellect devourers (those that survive the wizard's alpha strike) need to get someone to fail a DC12 and roll average or higher on its 3d6 intelligence attack. At this point, the cleric probably has greater restoration, and the wizard can keep slinging fireballs or setting up walls of fire in choke points while the fighters use their multiple attacks to hit the low AC low HP enemies from afar.
Even for a level 20 party of 4, a group of 15 CR2 creatures (27000XP) is beyond a moderate (22800) encounter, and it only takes 1 intellect devourer to be successful to set up the next for a body swap, but at level 20 where this scenario starts to make senes, the wizard had better have Wish prepared, or the cleric has True Resurrection prepared. Any group of 15 CR2 creatures is something worth running away from or at least having a decent strategy before engaging. Even 15 ogres, with their higher to hit modifier, damage and hp could be a real threat.
While the guidelines are not perfect, they have gone through play testing and are useful as guidelines. In some of these more extreme encounters, a playtest using copies of your character's sheets before the game might be worth running. That way, you know if the encounter will be too deadly. From all of my experience so far, the guidelines give a good indication of the difficulty of an encounter and how many of the party will be face down on the floor.