This is pretty much everything I remember about enchantments from when peeps were testing damage formulas and such last year:
- A character armed with an unenchanted, physical damage-only weapon deals purely physical damage with basic attacks, regardless of class. Their damage formula is essentially ((Character's Physical Attack) + (Weapon's Physical Attack)).
- A character armed with a permanently-enchanted weapon deals physical damage and also deals magical damage of the element of the weapon. Their damage formula is essentially ((Character's Physical Attack) + (Weapon's Physical Attack) + (Character's Magic Attack) + (Weapon's Magic Attack)).
- A weapon that is enchanted by a spell like a Boon or Affinity spell deals physical damage as well as magical damage of the element of the spell. Affinity level spells also add a percentage damage bonus based on the wielder's (not the caster's) magic stat.
- If a permanently-enchanted weapon is enchanted by a spell, the spell takes priority. If you're wielding a holy-elemental sword like Ascalon and a Mage pawn casts Fire Affinity on you, your sword is now fire elemental for the duration of the spell. All holy damage is lost, and your attacks are now 100% physical+fire.
- It's virtually always preferable to equip permanently-enchanted weapons since it gives you your character's Magic Attack as essentially a free bonus. In a hypothetical situation in which you're choosing between, say, a sword with 500 physical damage or a sword with 250 physical damage and 250 magical damage the enchanted weapon will do more damage in the vast majority of cases. There are some edge cases to this rule, and comparisons are never that direct, but as a default assumption enchanted weapons are typically stronger than their unenchanted counterparts.
- Individual skills can have their own damage formulas which operate independently of the equipped weapon. For example, Mystic Knight's Great Cannon uses about a 40/60 Physical/Magical damage split regardless of what you're wielding. This is probably what the person on the wiki was talking about.
That's most of what I can recall. I think I had 8 points in mind when I started this post but after 6 I can't seem to remember any more, so I'm just going to hope that what I managed to dredge up is enough to answer your questions.