"I feel that part of the reason for using a program like this is to get inspiration, and a big part of that is going 'outside the box' so to speak. So the flexibility regarding mixing of scales, modes, progressions and structure is an intended feature, not a limitation."
Yes, I thought that this was your intention and I appreciate in general. Its just more comfortable if you take different parts from different software if this is clear and simply stays "in tune". For example, one other software I use can import and recognize chords and then you can generate additional parts but for this its needed that you know the root and scale.
Other programs ? Lots of :-). I am really kind of addicted by any kind of generative stuff in this way. Mostly I use it inside DAW, so Captain Plugins, Orb Producer and lately InstaComposer (just to mention a few). I have Wotja too, which is the by far most develloped for any Ambient stuff but really complex and hard to get into. I prefer some simple stuff (for the user and the handling) like your tool in general cause it should be fun to use.
At the moment I cant really judge your program in comparision, for this I think I will have to follow your advise, generate a bunch of songs while playing around with the settings and then see what I can make out of it in a DAW.
Will sure be back with some comments when this is done :-)