As it says in the summary it's irrelevant if you define --disable-checks or --enable-checks, #define XFCONF_ENABLE_CHECKS 1 will be written to config.h anyhow. It works as expected if you remove the standard argument in configure.ac, but I don't know enough autoconf to do it in The Right Way.

Would still be nice to be fixed, because xfconf spams my terminal :/