Steps:
1) Install an unpacked extension with the following manifest:
{
  "name" : "Extension",
  "version" : "1",
  "manifest_version": 2,
  "optional_permissions" : ["*://*/*", "bookmarks"],
  "background": {
    "scripts": ["background.js"]
  }
}

2) Go to the extension's background page console and request for the optional permissions as follows:

perm = {
  "permissions" : ["bookmarks"],
  "origins" : ["http://*.example.com/*"]
};

chrome.permissions.request(perm , function(granted) {
  console.log("granted " + granted);
});

3) Ensure using chrome.permissions.contains that the permissions were granted.

4) Remove the granted permissions

chrome.permissions.remove(perm , function(remove) {
  console.log("remove " + remove);
});

5) Ensure using chrome.permissions.contains that the permissions were removed.

6) Restart the browser.

7) See the Details for the extension. The extension still has permission to example.com.

8) Go to the background page console.

9) Using chrome.permissions.contains verify that the extension does not have the bookmarks permissions (correct) but still has host access to example.com (incorrect).