The behaviors here are different across the Isolation Level settings, but in any case, it's simply how Factorio behaves and there's nothing that this mod can do about that.
maybe something good to ask developers on the modding thread then? Considering that undo works between surfaces/planets, it could be interesting to have blueprint world act as another planet?
If you use No Isolation, then the undo queue is preserved; if you use Full Isolation, then it isn't. Based on what I know about the internals, I doubt that this would be considered as a possible change. It is how it must work.
