I can't believe it has been almost 2 years since the original post and this hasn't been looked into.  I would love for a developer to see my current project I am working on.  They would for sure look into being able to create a legit credit memo with credit memo number number for these extra payments. Unreal what I have to do to provide a legit credit memo to a customer for them to use for a future order. 

#MAKECREDITSCREDITMEMOS!!!!