I'm likely to annoy people by saying so, but in my opinion, no there is not any significant difference between versions 5 and 6 of Burning Rom and Express. At some point 5 will be missing support for newer drives that 6 will include, and 6 does let you burn longer filenames than 5 does. Also, 6 supposedly has a new burning engine. But in my view, from an end users' perspective version 6 of Burning Rom and Express is primarily a minor
freshening of the GUI. And for at least the first several releases of 6, 6 had many more bugs (both in the engine and the GUI) than 5.
Ahead may finally be straightening this out. Sometime I'll have to try the latest release 22.214.171.124 that just came out a couple of days ago to see if they really have made progress. But since 6 doesn't offer much new, I'm not too motivated to mess with it.
Of course, as you noted, 6 does include some other programs that 5 doesn't have that may make it a worthwhile upgrade for some.
As for InCD, I can't say whether or not it mixing the versions of Nero will cause it grief. So many things cause it grief that it would be hard to tell what is to blame when it fails...