Use `UpdateAllowUnknown' for non-model related parameter. (#4961)

* Use `UpdateAllowUnknown' for non-model related parameter.

Model parameter can not pack an additional boolean value due to binary IO
format.  This commit deals only with non-model related parameter configuration.

* Add tidy command line arg for use-dmlc-gtest.

tests/cpp/test_logging.cc

@@ -53,6 +53,7 @@ TEST(Logging, Basic) {
   output = testing::internal::GetCapturedStderr();
   ASSERT_NE(output.find("Test Log Console"), std::string::npos);
 
+  args["silent"] = "False";
   args["verbosity"] = "1";  // restore
   ConsoleLogger::Configure({args.cbegin(), args.cend()});
 }