Custom app keyboard shortcuts: different commands with the same name
You can spell out the exact &quot;path&quot; to the menu item in question using the  &quot;-&gt;&quot; separator when you enter a value for the &quot;Menu Title&quot; in System Preferences. So, in your case, instead of &quot;Left,&quot; you'd enter &quot;Arrange-&gt;Align-&gt;Left&quot; (without quotes) as the menu command in System Preferences.
Source