Masonry chimney flashing

I’m having a true masonry fireplace built in a new construction residence. The chimney has a clay flue, surrounded by typical house brick through the roof, all the way to the top of the chiminey. The mason built a shelf about 1’ below the roof line to set the full width stone veneer on. The stone veneer also passes through the roof to the top of the chiminey.

The metal roof installer wants the stone stripped from the brick and wants to step flash from the brick through the stone.

The mason contends that cutting the stone for flashing is correct. Stating that breaking up his mortar and stone joints with flashing can affect the structural integrity of the stone veneer.

Roofer is willing to cut stone to flash and mason is willing to remove stone from entire chiminey for step flashing at my direction.

If the stone were to be removed, I’ve considered a relief angle, but there’s nothing structural to attach it to, so it likely adds little value.

Need a little help from the experts here. Thank you

I will have to disagree with the mason here. While I know they don't like a kerf cut into their beautiful stone work, it is acceptable and is the most minimalist approach to being able to counter flash the chimney without taking stone out.

In a perfect world, the stone is removed and the metal can run right up the substrate of the chimney and then be counter flashed to as to eliminate any ability for moisture to perc through the formation, but that requires more dismantling of the chimney.