Hi Tonnie. Interesting question. I've had the same issue making backing tracks for Kurt Rosenwinkel numbers and other modern stuff.

I'm not sure a programme like BIAB, amazing as it is, will ever be able to cope with really wierd note-stacks.

For example, just putting a C triad over a Db triad (a fairly common modern jazz harmony) gives you:

Dbmaj7(#9 b5) (Notes: Db F Ab C E G)

I only have experience with BIAB RT's, but my approach is:
a) listen to what I'm trying to emulate
b) listen to what BIAB does with different options, especially given the chord that comes next.

In the above example, I might end up writing C/Db, or Dbalt, or Db7#9.

Have you found other workarounds? Best - Andy