Ninja on mac and win should also read CFLAGS/CXXFLAGS.

pylib/gyp/generator/ninja.py

 # Copyright (c) 2013 Google Inc. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 import copy
 import hashlib
 import multiprocessing
 import os.path
 import re
 import signal
@@ skipping 788 matching lines @@
       if not pdbpath:
         obj = 'obj'
         if self.toolset != 'target':
           obj += '.' + self.toolset
         pdbpath = os.path.normpath(os.path.join(obj, self.base_dir,
                                                 self.name + '.pdb'))
       self.WriteVariableList(ninja_file, 'pdbname', [pdbpath])
       self.WriteVariableList(ninja_file, 'pchprefix', [self.name])
     else:
       cflags = config.get('cflags', [])
+      cflags_c = config.get('cflags_c', [])
+      cflags_cc = config.get('cflags_cc', [])
 
-      cflags_c = []
-      cflags_cc = []
-
-      # Respect environment variables related to build, but target-specific
-      # flags can still override them.
-      if self.toolset == 'target':
-        cflags_c = (os.environ.get('CPPFLAGS', '').split() +
-                    os.environ.get('CFLAGS', '').split())
-        cflags_cc = (os.environ.get('CPPFLAGS', '').split() +
-                     os.environ.get('CXXFLAGS', '').split())
-
-      cflags_c.extend(config.get('cflags_c', []))
-      cflags_cc.extend(config.get('cflags_cc', []))
+    # Respect environment variables related to build, but target-specific
+    # flags can still override them.
+    if self.toolset == 'target':
+      cflags_c = (os.environ.get('CPPFLAGS', '').split() +
+                  os.environ.get('CFLAGS', '').split() + cflags_c)
+      cflags_cc = (os.environ.get('CPPFLAGS', '').split() +
+                   os.environ.get('CXXFLAGS', '').split() + cflags_cc)
 
     defines = config.get('defines', []) + extra_defines
     self.WriteVariableList(ninja_file, 'defines',
                            [Define(d, self.flavor) for d in defines])
     if self.flavor == 'win':
       self.WriteVariableList(ninja_file, 'rcflags',
           [QuoteShellArgument(self.ExpandSpecial(f), self.flavor)
            for f in self.msvs_settings.GetRcflags(config_name,
                                                   self.GypPathToNinja)])
 
@@ skipping 1214 matching lines @@
           arglists.append(
               (target_list, target_dicts, data, params, config_name))
         pool.map(CallGenerateOutputForConfig, arglists)
       except KeyboardInterrupt, e:
         pool.terminate()
         raise e
     else:
       for config_name in config_names:
         GenerateOutputForConfig(target_list, target_dicts, data, params,
                                 config_name)