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Born protectors salamander strat allows you to declare a unit that is not being charged to be able to overwatch on a unit that is charging a friendly unit within 12" As if it were a target of that charge

If the enemy charging unit has the ability to prevent overwatch can Born Protectors give the ability to overide the no overwatch ability?

Need exact wording here I think. If the charging unit says something along the lines of "no overwatch may be fired at it" than no. However if the charging unit says anything like "the unit they charged" cannot fire overwatch, than yes.
For example: Banshees Masks; "Enemy units cannot fire Overwatch at this unit". it says enemy UNITS plural, so the strat would not work.

Is that not obviated by "As if it were a target of that charge"?

The unit that is being targeted "As if it were a target of that charge" cannot fire overwatch if the unit charging has a rule that prevents it from having overwatch fired at them.