This metallic (creaking or knocking) noise was constantly present whenever I brake, accelerate or drive over bumps - like the door was shifting a little and latch was hitting body metal or else.

How I solved it: the sliding door has 2 latches front and rear. The rear one was slightly misaligned by height. So I adjusted the door height by turning 10mm bolt that holds the rear slider on the door (with the spring on it) - sorry I don't know how it is called properly. It can be easily adjusted by several mm up or down. After that the sound disappeared.

Hope it will help someone with the same problem.

 

Here some more information, there was a TSB for this problem.
SUBJECT:
Sliding Door Lower Hinge Assembly Grinding Noise
OVERVIEW:
This bulletin involves removing and replacing power sliding door lower hinge assembly.
MODELS:
2008-2009 (RT) Town & Country/Grand Voyager
NOTE: This bulletin applies to vehicles equipped with power sliding doors (sales
code JRA and JRB) built before February 02, 2009 (MDH 0202XX).
SYMPTOM/CONDITION:
Some customers may experience a grinding sound when opening and closing the sliding
door.
DIAGNOSIS:
Open and close the sliding door multiple times. Assure there are no obstructions in the
track and listen for a grinding sound originating from the lower track of the door.
If the above symptom/condition is experienced or can be verified, perform the Repair
Procedure.
PARTS REQUIRED:
Qty. Part No. Description
AR (1) 05020920AC Assembly, Right Lower Hinge
AR (1) 05020921AC Assembly, Left Lower Hinge