I have found a simple workaround: I
include Makefiles which I made from the starting monolithic Makefile.
I am putting split Makefiles in a separate git project, that contains only them.
I am referring to those Makefiles from root project and I have them locally via git submodule. A bit more work - yes, but it allows me to have trivial "root" Makefile and all hard (quite often - repeating) logic in the separate project.
Example of how I made this work: