Even once one adds support for rule-configs with, features-override fails to work with Rules. The problem is that rule-configs are not simple data-objects, but classed objects including protected properties and Iteratores. e.g. doing a foreach over a rules-config doesn't give you all properties of it (but all nested actions).
Doing manually object-diffs for such objects like rule-configs won't ever work, so ideally one could just skip all the diff-magic and just export the overridden rule in a alter hook. That would work just fine in case of rules.
Maybe, it would be a good idea to allow people to choose whether overrides should behave that way anyway, as if mostly everything changed I'd prefer a complete override-export anyway as it is more stable, i.e. it won't break if the original export changes arbitrarily.