I apologize if this is againts your design philosophy, my idea is quite simple:
1. just put used chords (or scale, sorry got confused here) beside column number. For example: 1/C 2/Em 3/Adim etc
2. This may means each instrument will have to be wider vertically since all notes has to be present, for that why not just use scroll list for instruments (excluding drums). This will also let people use more than three instruments per block (which is another disapointment I just discover).
3. Here I see that for example at C major chord you remove F and B note. That's brilliant because that way inexperienced people wont accidentally make minor (sad) rythm with major scale. To maintain that simplicity while allowing all notes to be present, simply darken note areas that shouldn't be present.
Honestly I really love the idea behind 1BITDRAGON, but when I use it...it didn't have many feature that i tought very basic and easy to implement. Sorry if this sound offensive, but i really like this little program but it still so lacking but i really love this so much that I want to contribute (i can do a bit of coding and music :D), but I guess we have our own work, but i'll help what i can :D. Keep up the great work pal.