Is my custom shower enclosure plan reasonable?
That’s a heavy duty sandwich.
I would probably leave the ply up.
I don’t use it just backer board. I would leave it up because of the holes in the barrier would be leak points.
In the past I have tiled directly to plywood 3/4 and thicker.
using thin set to bond the backer to the ply and then screw them together this will make a very solid base.
once all the moisture from the thin set and grout are gone everything will be fine. Make sure to seal your finished job and that will last for 50 years.
I have seen tile on Sheetrock last 30 years and if it would have been sealed more often It could have lasted longer.
Thin plywood flexes with moisture changes I would not be concerned about that at this point.
Keep on going it looks like you are going to have a solid base and that is best for tile.