extconf.rb: Don't call pkg_config when using bundled libraries

This patch changes to call `pkg_config` only when `NOKOGIRI_USE_SYSTEM_LIBRARIES` specified,
because `pkg_config` isn't required when using bundled libraries.

And this works as workaround for the bug in 2.0.0-p0, 195, 247: https://bugs.ruby-lang.org/issues/8595

2.0.0-p{0,195,247}'s mkmf modifies `$LDFLAGS` after calling `pkg_config`. (Already fixed in upstream.. waiting for next release)

`pkg_config('libxml-2.0')` removes `-rpath` that added by extconf.rb, so compiled binary will be linked with system's installation.