Help with great weapon fighting. Designer required

Quote from Natrel >>

It's not that simple, because Shillelagh, and other edge cases. Nobody in their right mind would use the weapon's unmodified damage die on a Shillelaghed weapon.
And if we consider this edge case, there's no reason not to consider other edge cases too.

 Then please go ahead and list the other edge cases we should be considering.

Holy Weapon is another example. 
"In addition, weapon attacks made with it deal an extra 2d8 radiant damage on a hit"
The source of this extra damage is the weapon, via a buff. The source of the buff is a spell, but the source of the damage is still the weapon.

Helm of Brilliance
"As long as the helm has at least one fire opal, you can take a Magic action to cause one weapon you are holding to burst into flames. The flames emit Bright Light in a 10-foot radius and Dim Light for an additional 10 feet. The flames are harmless to you and the weapon. When you hit with an attack using the blazing weapon, the target takes an extra 1d6 Fire damage."
Again, this is a weapon buff. The source of the damage is the weapon, via a buff applied by a magic item.

These are not like Hex or Hunter's Mark. They effectively modify the weapon to make it deal more damage. And as far as Great Weapon Fighting, Savage Attacker, and other similar feats, "weapon's damage" means "weapon's current damage". Not "weapon's previous damage" or "weapon's base damage" or "weapon's unmodified damage" or whatever you want to call it.