Interesting find! I remember the discussion on this as well - I have an IWC Ingenieur AMG Chronograph (which IIRC you saw a beaten up version and thought 'fantastic' ) and initially had thought the indices were applied.
I have more than once been staring at the damn thing to figure out if it is stamped or not - my hesitation was due to the production numbers being much lower than the Portugiese and a 'limited' edition. However I reckon it is stamped. Something about it makes me think it is not applied.
I'm not sure about the bulked up 'newer' in house and pricey Ingenieurs to compete with AP ROO, maybe applied?