Seeking through the bootstrap script and found this:

  CC=*) CC=`cmake_arg "$1"` ;;
  CXX=*) CXX=`cmake_arg "$1"` ;;
  CFLAGS=*) CFLAGS=`cmake_arg "$1"` ;;
  CXXFLAGS=*) CXXFLAGS=`cmake_arg "$1"` ;;
  LDFLAGS=*) LDFLAGS=`cmake_arg "$1"` ;;

Looks like invoking ./configure CFLAGS="-Werror=vla" will do.