Hi there!
No, currently all changes made to the characters need to be done inside the generator scene. What can be done, is whenever you open the generator with a character that already uses pieces from that generator, the scene will automatically start with those pieces already drawn.
The thing is, when you use a generator and applies it to a character, the character will only have a KEY that will point out to the configuration(the pieces he used) on the generator. Because, if every character has stored all pieces individually, it will make the same file too big.
BUT, it does seem a nice feature to add, meaning a way to use plugin commands to change the character pieces. So I will put that on my to-do list.
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About the note tag, no. The only way to a character starts with preset pieces, is by creating a generator with default pieces already drawn, and applying it to the character.
On theory, you could do everything above using script calls, but it will not be easy for the user. I will see what I can about those two requests, But I can't say to you now when I will take a look into these.