Hi Bomaht,
I have the PDB and FC sitting stacked on my quads, about 2cm distance (less than an inch). I am powering it from the PDB's 5V BEC with a short connector (about 3inch, 7,5cm). It should be hard to get into trouble with a short cable, as long as your power source (BEC) delivers a good signal in the proper range for your FC and receiver (the FC output is not regulated). The only issue I know is, when you use long cables with bad quality and/or too small diameter, the signal loss then could be too much. I have that problem with one of my FPV cams, I had to shorten it, and will replace it by a better quality cable.
The problem with such a setup is very likely the magnetic compass: my internal compass turns red the moment the quad takes off.