Problem
CMake provides a built-in flag CMAKE_SYSTEM_PROCESSOR to specify the target platform for the build.
https://cmake.org/cmake/help/latest/variable/CMAKE_SYSTEM_PROCESSOR.html
CMAKE_SYSTEM_PROCESSOR flag is derived from environment variables PROCESSOR_ARCHITECTURE and PROCESSOR_ARCHITEW6432. And for emulated CMake, the environment variables could be set to AMD64 or IA32 and CMAKE_SYSTEM_PROCESSOR derives the wrong value.
And if your CMake project uses CMAKE_SYSTEM_PROCESSOR for platform-specific configuration it might fail.
Solution
You can use native CMake. There are no official CMake binaries for Windows Arm64 yet but can be generated from the source https://linaro.atlassian.net/wiki/spaces/WOAR/pages/28684353912/CMake#Build-from-source