For hordes, its that there's a significant combat disparity between early marines and humans, despite the small amount of bonus xp the humans get. For low xp adventures, like starting a group out and all that, a Chaos Space Marine is easily capable of handling twice the punishment and then some. They've at least one and a half times the wounds, start with power-armor, and generally have a TB five points higher.
So, yes, its an artificial mechanic intended to keep the "skill guys" from getting utterly annihilated in the first few fights, which kind of enforces less-than-ogryn intelligence on those fighting the party. Later on, here's no longer any reason to treat them with kid-gloves. After all, a late-game Heretek is possibly even *more* of a
walking humanoid-ish tank, sometimes with even heavier weaponry.
One thing we did in a game was force the humans to take Ancient Warrior for fluff reasons, but gave them an extra 1000xp [more than what Ancient cost], and allowed the Human version of all affected Legion Weapons, as well as Power Armor or LPA, to get the same rarity-buff the legion equipment gets. Starting bolters were made combi-weapons to placate the marine players, and everyone was satisfied. The Warband's Heretek was just as old and trustworthy, and had access to the Lathe Worlds mechanicus implants for starting gear; anything past character creation was gonna have to be torn right off its owners though of course. The Demagogue had like two gun-skulls and a heavy-weapons servitor willing to take hits for him right off the start as well.
Given these boons there was no need to pull punches on the party whatsoever. Horde combined-damage bonuses and all that were out in force, and so the players thought twice about wading into such a battle. I'll admit we probably should've thought it over thrice instead, but hey.
As for bolt of change… Really, anything firing those is a bloody tank-buster. You may as well be firing off a lascannon, it'll be less devastating. This unfortunately means that there's not much the party can do unless they get to plan for the encounter ahead of time; you'll want some protection against psychic powers. Though; its a bolt, which means it can be dodged or shielded against just the same as lascannons. Technically, someone lucky enough to be not too far away and have one of those amazing necron distortion shields could reflect the damn thing back as well. Anyone actually hit by it is utterly screwed, though, unless somehow you rolled all ones on the damage.