The improved smithing technology and knowledge is a good point but doesnt quite belong in a clearly magical element to the game, we can put that down to each Realm's skill at regular metalworking.

Runes are a cool way of making one method of enchanting possible. We them can look at where Runes came from, perhaps Dwarven influence or something else. Of course Runes are still Magical in nature, which implies that there could be further ways to enchant a piece of equipment.

In the Warhammer Fantasy universe, there are mages and sorcerers who can make armour or weapons infused with magic (Commonly Elves) And then there are Dwarves who instill their weapons with Runes, which are forged from Magic, of course.

We live in a world with reanimated skeletons and zombie monsters roaming around. That is necromancy, which is again Magic.

We also have Portals to Hell and to the Void where there are teleporting demons and a Dragon.
Not too far fetched to think that the lore for Enchanting is due to Magic.

Where this magic comes from is another question entirely.

I don't think that that is necessary, there is no reason that there couldn't be more than one way to make magical weapons. If we force people to only use one way it limits the creativity people have with their lore

Personally I think the different sources of enchantment for each race is quite fascinating and the most balanced proposal

Agreed. Now, certain parts of other's lore might be regarded by some as "mythical" perhaps, much like certain religions are. For example, if someone's enchanting knowledge was said to have been dictated by a magical Magikarp that flew out of the ocean, some might see this as more myth than fact.