Just a guess as I am not in the industry but I would imagine has to do with the photoresists and masks - perhaps we don’t have ones that work with X-ray. Not much good using a wavelength that passes through or is unabsorbed by the resist material!
The machines that create the masks are also not very fast. A mask is created by firing an electron beam which is a sequential process.
If you were limited to one wafer per mask then not only would each chip cost tens of thousands of dollars you would also only be able to produce a single digit amount of wafers per year.