TL;DR: Edron used to be a special place that sold special runes, the game evolved but the old NPCs trade lists were not changed.
NPCs started selling runes in Tibia in the Summer Update of 2005 at version 7.5. Until then, runes were only available from druids and sorcerers that created and sold them. Back then, the game was very different, the meta-game of hunting and getting experience was completely different, and mages were not as dependant on and did not use as many runes as they do today. That change was made to prevent a rune shortage due to the addition of Soul Points, by the way, not to change the meta-game.
Anyway, CipSoft chose to keep some runes slightly harder to buy than others, such as Energy and Poison Bomb Runes. These runes could be bought in Edron, but not in any other city. For quite some time, Edron was the only place that sold these exclusive runes. The Noodles Academy of Magic was always a special place where Tibian Magic knowledge can be found. Perhaps to avoid making the only place Tibians would go for runes, however, they decided against selling common runes there - the Noodles Academy wouldn't want to waste their time selling trivial runes you can find anywhere, would they?
This situation lasted for many years, until 2013 when Roshamuul was created. It was only then that a second (and third) "special" runes seller was added. Both of them only sold the Edron-exclusive runes though, so no Avalanches or SDs. A year goes by and Rathleton is created. For the first time, an NPC sells all existing runes: Mordecai. Almost ten years after NPCs started selling runes, the game now was very, very different. Players now buy runes in hundreds to hunt Roshamuul Valley, Prison and the new Oramond Dungeon. Getting direct access to Rathleton from the Oramond boat has its own challenge and is not trivial for a low level (of that time).
After that, most new Magic Shopkeepers added sold all types of runes. Many players were already used to buying runes not available in a given town through the market for a minimum price difference, or maybe to stock thousands of runes in their Depots (then Stash) just to make things easier. The old NPCs were simply never changed. Players were already used to them and even though I'm sure some players asked, CipSoft probably decided to keep existing NPCs as they were, "just because".
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