How to configure pkexec to not ask for password?

It's improper to say that: "It seems that on Ubuntu, calls to sudo from the GUI are somehow being intercepted by pkexec". pkexec doesn't have much in common with sudo. In contrast with sudo, pkexec does not grant root permission to an entire process, but rather allows a finer level of control of centralized system policy.

Now, if you want to run a GUI application without being asked by a password by pkexec, this is not difficult to be done. Let's take for example GParted. When you open it, you will see the following dialog window asking you by a password:

Click Details and the dialog window will look now like:

From here all you have to do is to open /usr/share/polkit-1/actions/com.ubuntu.pkexec.gparted.policy file using for example the following command:

gksu gedit /usr/share/polkit-1/actions/com.ubuntu.pkexec.gparted.policy

and change the following lines:

      <allow_any>auth_admin</allow_any>
      <allow_inactive>auth_admin</allow_inactive>
      <allow_active>auth_admin</allow_active>

with the followings:

      <allow_any>yes</allow_any>
      <allow_inactive>yes</allow_inactive>
      <allow_active>yes</allow_active>

Save the file and close it. Next, when you will open GParted you will not be asked for a password anymore.