ESET HIPS Smart Mode can effectively stop the problem if the custom rule is created I mentioned in my post.
The technical reason is that ESET’s HIPS logic is designed to honor all custom user rules, regardless of whether the system is in Automatic, Smart, or Learning mode. While Smart Mode is programmed to be "quiet" and only notify you of very suspicious events by default, adding a specific manual rule creates a mandatory check that overrides the standard automated filtering.
In HIPS, manually created rules are evaluated alongside pre-defined system rules. By explicitly creating a rule to monitor or block modifications to %SystemRoot%\System32\, you are instructing ESET to ignore its "Smart" reputation-based whitelist for that specific path.