Farmer,
With the normal sill to window distance, your CBU ends against the front of the frame. Then, your waterproof membrane ends where the CBU ends. Then, maybe, you caulk the membrane to the window before you tile, if you notice this potentially bad situation....If you don't, or if that caulk cracks, and the caulk between tile and window above that cracks, then you have a nice vertical crack for water to travel downward into the walls.
If you still can, I recommend removing the sill 2 x 4 by pulling/cutting the nails. Then cut the jack studs that support it at a slight angle, cutting them down just enough that the finish tile will be able to slide under the window frame. (may have to power plane the protruding front corner of the sill after reinstalling it).
If the tile finishes under the frame, and your caulking is now between the bottom of the window frame, and the top of the tile, and there's tile heading upslope behind that caulking joint, then if the caulk cracks, well, water doesn't run uphill (usually).
Brian
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