I can't speak for Sync 3, but Sync 2 (which was ironically Windows-based) actually is isolated.
There is no information from the driving computer (e.g. speedo, mileometer, etc.) that propagates into the Sync 2 system anywhere at all. Even the controls on the steering wheel are separated - cruise control etc. on the left,and entertainment volume, phone etc. on the right. You have the clock on one but not another, the GPS on one but the instrument speedo on the other, and so on.
The Sync 2 handles bluetooth, wifi (for sharing local connections only), satnav (entirely offline) and - oddly - aircon and as far as I know contains no connection to the car's buses. If you want to replace the Sync 2 with Android units, you basically have to plug in an OBD adaptor to get anything like that. You don't have to plug in to control aircon, for instance, but you do if you want OBD information.
Given that you can upgrade the Sync 2 to the Sync 3 in many models, I would suspect that this is actually the case going forward too, unless such an upgrade involves a far more drastic rewire than people are letting on.
And I have personal experience of the Sync 2 because I had the unit fail on me while driving. At first the music was skipping and being odd, then I lost control of the entertainment. Then the unit powered down and I lost aircon. But at no point was the dashboard computer (the one behind the steering wheel that handles and displays MPG, driving settings, etc.) affected, and nor were any driving functions.
Turned out that the SD card just needed replacement, but the whole entertainment system just bugged out and fell over, while I was driving along happily.
Apart from that one incident (resolved with a non-corrupt SD card), it was pretty solid.
But Ford Sync has been through a number of iterations now - QNX, Windows, etc. I'm just going to leave mine on Sync 2 until the car dies, I think. I don't even really use the satnav any more as it costs £150+ (or some piracy) to update the maps and they only surface once every year or so. They can't quite seem to get it right and I don't think throwing it all out and starting again each time is helping.
That said, it does everything I want it to do which is connect to my phone, play music, turn on the air-con and get out of my way.