Disable setting incognito prefs for extensions for now.

chrome/common/extensions/docs/static/experimental.proxy.html

 <div id="pageData-name" class="pageData">Proxy Settings</div>
 
 <!-- BEGIN AUTHORED CONTENT -->
 <p id="classSummary">
 Use the <code>chrome.experimental.proxysettings</code> module to manage Chrome's
 proxy settings. This module is still experimental. For information on how to use
 experimental APIs, see the <a href="experimental.html">chrome.experimental.*
   APIs</a> page.
 </p>
 
@@ skipping 200 matching lines @@
   mode: "fixed_servers",
   rules: {
     httpProxy: {
       scheme: "socks5",
       host: "1.2.3.4"
     },
     bypassList: ["foobar.com"]
   }
 };
 chrome.experimental.proxy.settings.set(
-    {'value': config, 'incognito': false},
+    {value: config, scope: 'regular'},
     function() {});
 </pre>
 
 <p>
 The following code sets a custom pac script.
 </p>
 
 <pre>
 var config = {
   mode: "pac_script",
   pacScript: {
     data: "function FindProxyForURL(url, host) {\n" +
           "  if (host == 'foobar.com')\n" +
           "    return 'PROXY blackhole:80';\n" +
           "  return 'DIRECT';\n" +
           "}"
   }
 };
 chrome.experimental.proxy.settings.set(
-    {'value': config, 'incognito': false},
+    {value: config, scope: 'regular'},
     function() {});
 </pre>
 
 <p>
 The next snippet queries the current proxy settings.
 </p>
 
 <pre>
 chrome.experimental.proxy.settings.get(
     {'incognito': false},
     function(config) {console.log(JSON.stringify(config));});
 </pre>
 
 <p>
 Note that the <code>value</code> object passed to <code>set()</code> is not
 identical to the <code>value</code> object passed to callback function of
 <code>get()</code>. The latter will contain a <code>rules.httpProxy.port</code>
 element.
 </p>
 
 <!-- END AUTHORED CONTENT -->