Well there are already 2 history stacks in krita, the brush preset history and the undo history docker. While the brush preset history docker is not a undo stack both are history stacks.
Having the layer states in the undo stack just seems like a waste, I only noticed recently that the states were not saved by themselves or not put in the undo stack and I actually never missed it.
About it confusing newcomers i don’t see how it could, have the undo stack as normal, they already cant undo layer states so the usual expected behavior is already set. I believe changing the behavior of something that already exists will cause much more confusion that adding something new that adds new functionality.
While I understand having 2 stacks is not very practical, to me feels better to separate both things. If the userbase asked for its removal before i believe there was a reason. I fear that just adding back will just make we go in circles in asking for a functionality and asking for it to be removed, maybe studying how people would use it and how is the usual workflow to be able to implement it in a way that is good for most cases. I think that would be better for the users than just adding it back with the cumulative undos.
Another suggestion that could be relevant is what MangaTengu said about having in the settings a way to toggle if the layer states are taken into account for the undo stack or not like a “feature preview”, if possible. For a first moment I think just giving the users options is more safe, see how they will react to the new feature and then if the acceptance is high ask if they want that to just be the normal behavior or not.