i have similar tree-containing-symlinks-to-one-thing - and i do it by symlinking each x to ../x ; and only the root x (of any tree) is a real thing (or missing, if it lives on some other device). Thus the structure is still tar/archievable.

Of course you can do things like these too:

$ MAKEFLAGS="-f /that/root/makefile" make

or (rude)

$ alias make="make -f /that/rooty/makefile"

but beware that adding another -f somemakefile will load both specified.

Apart of it, my biggest grievance with make is that it cannot handle spaces in names. By design.