I understand your concerns.
Well, the current version of EndNote has many dangerous tools to ruin the whole library and citations.
However if a user knows what he or she is doing, then it will go fine.
I want to highlight that the proposed function for automatic insert function should work only if there are no ambiguities and only a single database record was found for the target citation.
Therefore I would suggest adding this.
Perhaps a separate button is too much, but a tick option would be fine.