Thanks for the excerpt. Attachments might not be the way to go then. But I'm sure @dseagrav has already has an idea how he wants to do it. If we have enough control over the docking method for stage separations, then having the stages "docked" will work pretty well, I think.
I understand. However, the difference is that we have different stages, separated in a certain sequence and they should still be functional in some way after staging. Right now upon separation there is a lot of code dealing with creating a new vessel, giving it some of the properties of the combined stage etc. Another example would be the Launch Escape Tower. If you don't jettison it during the ascent, then it messes with the staging sequence. The mesh used to just vanish when the S-II stage is separated. The physical properties aren't right etc.
All this code making sure everything works despite the LET being attached could be eliminated. That's why I think it is an improvement and simplification to have the stages separated from the beginning. Of course this only applies to NASSP.