The atomic supports for this toolchain is broken:
A minimal test case:
guix shell arm-none-eabi-toolchain -- \
bash -c "echo '#include <stdatomic.h>' \
| arm-none-eabi-gcc -x c -o /dev/null -c -"
Something similar found online:
However no solution.
This happens with all versions of the arm-none-eabi-toolchain
Jean-Pierre De Jesus DIAZ