As Ludovic wrote

>  Actually libc’s configure doesn’t use the normal AC_CONFIG_SUBDIRS
>  mechanism, and instead runs add-on configure scripts by itself, without
>  arguments AFAICS.

The part responsible for this is in the attached file and specifically the part:
>      libc_add_on_frag=$libc_add_on_srcdir/configure

I was thinking of modifying the configure script so it would use the AC_CONFIG_SUBDIRS mechanism and configure all the addons with the flags passed in the glibc configure.
Then I would apply the patch in a patch-phase before configure gets called in guix.

What do you think?

Manolis