Well, for skalibs in particular, that happens to work, since you (for
some reason) add -fno-stack-protector to CPPFLAGS, and CFLAGS happens
to come after in the compile rule. But for e.g. s6 and s6-rc, you
append fno-stack-protector to CFLAGS, so it doesn't matter what CFLAGS
contained at configure time; your setting overrides that (and not the
other way around).
Hm, that is a problem indeed. The goal is always for the user CFLAGS to
override the automatic CFLAGS. I'm going to fix that.
Thanks for the report!