I have not checked the speaker distances but assume that they would affect PCM and DD streams equally.
Gianni,
I can tell you from recently running the 565 Z3 V6.0 for a couple of months that they do affect them equally. The time alignment done in configuration is applied to the output of Discrete Digital, Analog Stereo and Analog Surround material out of the 565.
FWIW, I experienced no such time alignment issues watching TV receiving PCM or DD via the Optical Output from my Smart TV. The Cable Box is hooked up via HDMI directly to the TV and I use the TV's SPDIF Optical output into the 565.
Perhaps try doing the same on your 565 if you are plugging it in directly from your Sky STB's Optical/Dig Coax SPDIF out... assuming it has an HDMI output to send to your TV and if your TV has an Optical out. I'm not familiar with Sky boxes since I'm not from the UK but I'd imagine most of them have similar connectivity to US digital cable boxes.
If you can do this, just make sure you set your TV's digital output settings to output all compressed audio without change (aka DD 2/0 or 3/2.1) otherwise it will by default convert everything to Lt/Rt PCM 16/48 which you don't want as you want the 565 doing the Lt/Rt downmix.
That's a pretty neat idea you came up with to use your 565 again. It's an awesome sounding processor for any use and I think it will serve you well in this re purposed usage.