[gclient_scm] Use --replace-all within set_config

Bug: 40942309
Change-Id: Iee6473e73fa7a0ce7ec33640c0d2fe8f49054c3a
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/5292943
Commit-Queue: Josip Sokcevic <sokcevic@chromium.org>
Commit-Queue: Aravind Vasudevan <aravindvasudev@google.com>
Auto-Submit: Aravind Vasudevan <aravindvasudev@google.com>
Reviewed-by: Josip Sokcevic <sokcevic@chromium.org>

gclient_scm.py

@@ -615,8 +615,10 @@ class GitWrapper(SCMWrapper):
                     config_updates.append(('push.recurseSubmodules', 'off'))
 
                 for update in config_updates:
-                    scm.GIT.SetConfig(args[0].checkout_path, update[0],
-                                      update[1])
+                    scm.GIT.SetConfig(args[0].checkout_path,
+                                      update[0],
+                                      update[1],
+                                      modify_all=True)
 
             return return_val