Could an aircraft 'hide' in the aircraft shadow of another aircraft without being detected or noticed?
Radar resolution is defined in terms of degrees of arc (or alternatively in steradians/solid angles) and as such, the further away from the radar, the larger volume is being sampled.  At altitude and some distance from the radar you should have a bit of leeway on how loose of a formation you can fly and show up as one contact on the radar display.  I'm not giving credence to the theory presented, but I am saying it is plausible that one aircraft could fly a formation with another and be detected as one airplane by a radar.

If the transponder is off, the aircraft you are following will not see you on TCAS  and if you are behind them you will be visually undetectable by the crew or passengers.  If you fly above them you will be clear of their wake, so I would put behind and above the best position to shadow.  A lateral offset might be safer, but if you stray too much, you might wander into the FOV of the cabin.
I can't see any way the following airplane would cause nav or com interference in the followed airplane.

The biggest threat to being detected in this scenario are being seen by other airplane.  If ATC calls traffic and you see two planes in formation instead, you would probably say something.  In the case of the airplane you refer to however, it was night and if you turn all of your position lights, beacons, strobes, tail lights and if there is no moon out you might escape visual detection by a third party.