SpaceX missions are also a lot shorter. Having one unrecoverable latchup a week isn't a big deal if your mission is 2 weeks long. If you mission is 10 years, it starts to become a problem (especially since some radiation damage can be cumulative)
>NASA and DoD are still baselining new platforms on incredibly expensive (albeit rad-hard) PowerPC RAD750 and similar
NASA and DOD have also been sending up Xilinx and Altera boards for ages (even the non space-grade ones). However you can get rad-hard ARM CPUs that are cheaper and more powerful than the ones in a Zynq board.