Well I just tried, reading that it's doable, according to section 4.2 of the manual.

So I added one line right after (build-system gnu-build-system) :
(arguments '(#:phases (modify-phases %standard-phases (delete 'configure))))

And logically the outcome changed :
phase `unpack' succeeded after 0.1 seconds
starting phase `patch-usr-bin-file'
phase `patch-usr-bin-file' succeeded after 0.0 seconds
starting phase `patch-source-shebangs'
phase `patch-source-shebangs' succeeded after 0.1 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.2 seconds
starting phase `build'
make: *** No targets specified and no makefile found. Stop.
phase `build' failed after 0.1 seconds
builder for `/gnu/store/s0diig2i0533r6sl7iib9pmskpx8ri4a-freefilesync-9.9.drv' failed with exit code 1
@ build-failed /gnu/store/s0diig2i0533r6sl7iib9pmskpx8ri4a-freefilesync-9.9.drv - 1 builder for `/gnu/s
tore/s0diig2i0533r6sl7iib9pmskpx8ri4a-freefilesync-9.9.drv' failed with exit code 1
guix build: error: build failed: build of `/gnu/store/s0diig2i0533r6sl7iib9pmskpx8ri4a-freefilesync-9.9
.drv' failed
arnaud@brix ~/guix_packages/gnu/packages$

Getting late tonight but tomorrow pointing directly to the provided Makefile might help ?

Cheers and thanks for reading so far :)