Gotta see the outside and know the layers.

Windows don’t belong in showers where Bubbas are doing the work. You have a disaster on your hands, outside and inside both.

Install the backerboard, waterproof, and tile up to/past the window. Install a Glacier White Corian sill over the existing with a good edge overhang and a drip slot on the bottom with returned ends which Corian jambs with Corian casing will die into. Silicone a Corian head jamb with casing into position and you've got a waterproof window. I'd charge you several thousand dollars, but it would never leak, need maintenance, or grow mold or mildew. And would look fantastic.

We were told fortiflash should wrap into stud area. That way, it would prevent any moisture from finding its way to studs. Silicone will not last from the many folks we have spoke to.

Outside is flashed correctly. The one issue is that the fortiflash does not wrap into the inside.

What waterproofing system is being planned for your shower? Cement board, tile, and grout are NOT waterproof. And where did you find the bubba that doesn’t have a clue who is hacking this up?

https://www.ceramictilefoundation.org/find-certified-tile-installers