I have also set the flash profile on my V6 for my system dedicated flash (in my case a Pentax AF-540FGZ). I noticed that when holding the Menu button in order to activate TTL pass-through, that I briefly see the information 'Pentax AF2' appear, then 'TTL Pass-through'.
Unless you have the FGZ II model, you should select the profile for the standard FGZ (just "AF540F", not "AF540F2").
But I am not able to control the Pentax manual power from the V6 controls. Am I right to think that if I deactivate TTL pass-through that I should be able to adjust the manual power output of the flash on the V6 from the V6 ?
Yes, just deactivate TTL pass-through and then adjust the power of the flash by pressing the menu button and simultaneous turning the dial.The flash still needs to be in TTL mode.