You are misunderstanding things. The Dungeon Master narrates and describes what the characters can feel, hear, see, etc. or act out the reactions of the environments or other characters. However, they do NOT narrate FROM a character's perspective. Those are different thing. For example, "Surrounded by darkness, you cannot see anything but you can hear something approaching" is different from "I cannot see anything, but I can hear something approaching". The first would be what a Dungeon Master, who usually play a role similar to the director / omniscient narrator, would state, while the later is what a character's perspective would be. The role of a DM and a player is supposed to be separated - even if the DM want to play a character and influence the story that way.
In this case, if we are to apply D&D rule since you mentioned it, the "you can feel the legacy of C'Thun's evil around you" would be the DM's description of what you feel. The rest would be description of the environment and the NPC. All of those are done from an (kind of) omnipresent narrator's perspective, not the player perspective.
Khadgar hasn't been always using Atiesh. He only started wielding it during Legion (WoD was supposed to be a look-alike according to UVG), it isn't too far-fetched for Med'an to have passed it to Khadgar offscreen. They have interacted before, after all. Moreover, the original restoration of A'tiesh was only done in-game during Vanilla - which might not even be canon anymore. Now, canonically, the first siege of Naxxramas was done by Darion (see "The Ashbringer" or in-game Ashbringer artifact quest text), and I'm pretty sure I never saw any Darion in the raid during Vanilla. This isn't the first time that the raids, lore-wise, aren't the same as the in-game raid we play. Blizzard said it: it's a matter of lore and gameplay segregation.
Again, regardless how you feel about the comic or if you think it's confusing, when Blizzard says it's canon, then it's canon and we can use it as a valid source. When they say "No, those comic books aren't canon any longer", then we can start arguing whether it's a valid source or not. As of now, it is. Except Med'an being the Guardian, the rest of the comics remain canon - for example, if you really want a speculation of how that could happen, it's possible that Med'an took the power, but never accepted the title Guardian, and the others agreed to go with it. There, done, the entire comic story remains the same.
(I'm not saying that was Blizzard's canon explanation. As of now, I'm not too sure what's their explanation either. However, that doesn't change the fact that everything in the comics are still canon except Med'an being the Guardian. Blizzard don't have to explain something they said / wrote - heck, they don't even have to make sure that "something" makes sense - for it to be canon)