Danfink, braces are difficult but important to fit well. Due to the rigidity of the triangle they make, small differences in length are critical. Even a sixteenth-inch can matter.

It would certainly be possible and good to use the seat/housing depth to create a perfect dimension, from your reference face or centerline as appropriate.

Personally, I think a 3x5 brace is a more pleasing dimension than 4x6 - perhaps you can resaw all your braces to that size?

Pete