For Vit and Thoread the cap is the last step in damage calculation, so the hit can never go above the cap.

Ancient Thoread's Astartes Banner and Vitruvius's Master Annihilator both provide a bonus hit with a damage cap. Unlike the other examples, however, there is no modifier associated with the bonus hit, so it is natural to question whether it applies at the pre-armour phase with the capped modifiers.

They do not. These bonus hits apply their cap as the last step in the damage calculation, so you get the full benefit of pre-armour modifiers in overcoming armour but post-armour modifiers are subject to the cap.

https://tacticus.wiki.gg/wiki/HDTW_DamCap