OK, I found a way by playing with it.
I first measured the interface on car side by a multimeter as proposed by the service manual - It's a four pin connector with +12V, GND, and a CTL signal lines connected.
The connector in Liberty/Cherokee is keyed or asymmetric with pin #1 on the straight edged side of it.
With ignition in ON position and FCV disconnected you can first check the car side interface rather easy by measuring +12V on pin #4, and some small voltage (by heart around 1 V) on pin #2 (CTL signal). Multimeter set in DC voltage range. The CTL signal is a PWM signal, hence the arbitrary output. Check also that pin #1 has good connection to ground.
If you can't find the battery voltage on pin #4, you have an issue with the voltage feed and there is a relay and fuse involved, but that's another story.
Power on test method, option 1:
I noticed that if you then cut the power, connect the FCV, and switch power back on (key in ON position), the ECU activates it (flap might move a bit, and you may hear some buzzing from it as a result of PWM control and mechanical slacks - this might also indicate a future failure if loud enough or flap really visibly vibrating). If you now try to move the flap (still power on, engine off), you can feel the resistance of the servo, and it will also return to it's desired position after you let go. Do this at your own risk, as moving the flap by force might damage the servo gears. The best part is that when you switch the ignition OFF, the flap moves briefly to a nearly closed position, and then returns to wide open, so you can really see that it's properly controlled and moving.
Power on test method, option 2:
I also noticed that if you connect the FCV while power on (key in ON position, engine off), the ECU detects it, and does some sort of self test by moving the flap nearly closed, then back open (as in powering off). Then you can also try to move the flap as in option 1. Note, that in addition to servo mechanics, the ECU might also suffer from connecting such components on the fly. However, I didn't seem to damage anything by doing it either way.
Voilà, seems to work. Should be an easy way to test the FCV also in place without removing anything but the charge air hose from FCV side.
Tested on Cherokee/Liberty CRD 2.8 2006, and hope this helps somebody else in any case.
Here's also a link (as long as it's available) to relevant service manual pages as long as they are available...