I'm impressed that ~20kV is possible with both windings on one PCB!
Only if there's enough clearance. You can't do 20kV layer-to-layer as far as I know, unless you get ridiculously thick boards.
Forgive my ignorance; I though X-Ray tubes are largely made of glass. I've never worked with them myself (and might be too chicken given high V and radiation hazards I'm not trained for).
You're correct. They are still mostly glass, but there are metal passthroughs, and on lower energy tubes you must have a beryllium window, otherwise the glass itself stops the x-rays from coming out.
Here's the tube I'm working with:


It's a "shoot-through" style anode, where the x-rays exit in a linear manner through the anode, rather than being emitted to the side.