Jervis gave a seminar at one of the GT heats at which he said that the 2 books would not be compatible. GW are making a point of not doing add on codexes any more, as you can see by stuff like the marine books all being done as full lists in one book. Effectively, this means that a totally new army is getting added to 40k.
This approach was more or less backed by the tournament players present, as it has often been these add on lists (whether in seperate books like Ulthwe or appendixes like Ulthwe) that have caused problems in the past. Better to have full lists that have been properly playtested as stand alone armies than mix and match army lists where you can cherry pick combos that were never originally intended.
In normal play you can do what you like so long as your opponent agrees. I imagine that in apocalypse people will be using CSM, daemons, renegade guard and titans pretty much as they like.
