How to make a transparent Glyph

The bug is with the printing/printer then. Showing something and printing something are two different things.
If the font works on screen but not on print it’s not the fault of the font.

One thing you can test: can you make sure that the fallback font has different shapes that the color layers. That way you can check what you are actually getting when printing. I suspect that the printer used the fallback font.