CMake does not naturally supports different C/CXX compilers in CMake Project. However, it does support "subdirs". Which means CMake understand that different project have completely different toolchains.

Just make an independent CMake for the MCU firmware and independent one for the SBC.
The third CMake will be your root CMake, it should add the others as subdirs and make the joint.

https://cmake.org/cmake/help/latest/command/add_subdirectory.html