[kintamanimatt]

They generally are separated, however the 787-8 is apparently an exception, having been granted "special conditions" by the FAA in 2008. [1] The A350 has a similar design and I imagine they've also have similar special conditions, although I haven't done more than a cursory search.

[1] http://cryptome.info/faa010208.htm

[jacquesm]

That's one interesting document. I find it hard to believe these are even negotiable, and given that the trend is towards more features and connectivity between systems that does not bode well for the future. You'd think that the FAA would hold their foot down on physical separation of those systems but that does not appear to be the case, you can connect the two as long as you then put in another layer protect the domains related to information and aircraft management.

Enfin, they presumably know what they're doing, personally I'd prefer for such a bridge to simply not exist.