I wish. The shield symbol still displays for both, and when using a mod that adds a new type of Flamer Fuel with 15 DT I immediately noticed a huge difference in damage against high armor targets like Super Mutant Masters and Brotherhood Paladins. Using a Flamer on a deathclaw is a complete joke unless their legs are crippled, then it's just a waste of fuel.

You might be right, it is probably just "burning" effect which ignores armour.