syscalls and STM32CubeMX
System call is the interface provided by OS.
As you mentioned, this is the programming on bare metal, which means no OS.
The syscall.c provided in this example is a reduced version of implementation, in hope to stub those “expensive” system functions and while provide a simple implementation to the other system functions, in this case for Standard Output.
As said, this example syscall.c is far away can be considered to meet wider requirements, so it shouldn’t to be included into CubeMX. It is only an example.