"Import > General > Existing Projects into Workspace" imports a project without modifying the settings. The Makefile is automatically generated when building the project (pre-build and post-build are added to the generated makefile)
"Import > C/C++ > Existing Code as Makefile Project" creates a new Eclipse generic makefile project (and not System Workbench project). It means that you provide your own Makefile so you can modify it.
By the way, If you really wanted to import a Makefile project, my advise to create a new project then copy/paste your sources into it.
New > C Project, select Makefile project and Ac6 STM32 MCU GCC toolchain.