Read the rulebook, plan for all contingencies and… Read the rulebook again.
If Box Barrage is played and a tank is hit with a flag result, does the tank take a hit?
On one hand a tank will always ignore the first flag rolled against it. On the other, flags cannot be ignored for any reason.
Ultimately, the Combat Card trumps the rules I think?
Yes, I think that's right, too. If you need support from the rules, I'd go by the last bullet point for Combat Cards on p.25 of the basic rules:
• In case of conflict between the basic rules in this book and a combat card, the rules of the card take precedence. However, terrain movement and battle restrictions will always apply, unless stated otherwise on the card.
I know that the rules for Tanks are in their own booklet and not found in the basic rules booklet. But I would regard the Tank rules as an extension of the basic rules for the purposes of resolving the conflict between the Combat card and the rules for Tanks.