but this specific case where you can define a whole family of commendations in one go would also automagically create a corresponding family of no-longer-identical sets of soldier bonuses.
Yeah, we have enough headaches with automagical commendations.
I'm not going to do automagical soldier bonuses... that's the very last option for me.
My preference would be to just stack them.
We do keep full track of them in the save file since the beginning, they can be duplicated (both via transformation and commendations).
The "non-stacking" happens when we calculate and cache the the bonuses per soldier (we didn't do that at the beginning, it was introduced later for performance reasons).
It could be that they stacked initially, I'll check the history tomorrow/later.