A quick update:
A user reported that cmdstan via cmdstanr works OK after adding
CXX="arch -arch arm64e clang++"
to the makefile flags.
So for cmdstan you need to add the following to to make/loca
l and rebuild cmdstan
CXX="arch -arch arm64e clang++"
For cmdstanr you need to run
cmdstanr::cmdstan_make_local(cpp_options = list(CXX="arch -arch arm64e clang++"))
rebuild_cmdstan()
and then everything should work fine. The next cmdstan version will handle this automatically.