Hi,
If you prefer using GNU Make, you can always patch the Makefile to change its layout and support multiple folders, however it is something for you to setup and test.
On our side, we have designed the MSBuild-based and CMake-based projects specifically to address numerous shortcomings of GNU Make, and advise using them instead.
MSBuild is fully compatible with CI/CD – you can simply generate a batch file with all commands: https://visualgdb.com/documentation/projects/msbuild/#standalone (although you would need to programmatically replace absolute paths in it and in the .rsp files).