It turns out that it’s the autogenargs:
autogenargs="--with-target=quartz --disable-video --with-font-backend=pango --with-gtk=2.0 --disable-geolocation --disable-webkit2 CXXFLAGS='-Wno-c++11-extensions' CFLAGS='-std=c99’"
eats the CXXFLAGS and CFLAGS set in .jhbuildrc. It needs to be
autogenargs='--with-target=quartz --disable-video --with-font-backend=pango --with-gtk=2.0 --disable-geolocation --disable-webkit2 CXXFLAGS="$CXXFLAGS -Wno-c++11-extensions" CFLAGS="$CFLAGS -std=c99”'
(Note that the quotes are flipped because single quotes prevents the shell from expanding the variables.)