Jonathan,

The Borates will not hold up to continued saturation. They are best for situations where there may be occaisional water incursion. Your copper flashing does not sound like a bad idea. One thing to consider in flashing will be how to retard water entry while providing plenty of areas for the water to exit - i.e. gooping up the whole joint may enchance, not retard decay.

Wish I had a better answer for you,

Andy