Well i for one prefer powerful checking tools over human checks as i do not trust humans in general (including myself)
This is why i stack pins with the knowledge that stacked pins are connected. (Their connection point is on top of each other -> the very definition of a connection in kicad.)
And as i described: Not stacking pins can easily remove some of the power from the electrical rule checker -> simply not worth the tradeoff. You gain the option to have a schematic checked by an unreliable (and inconsistent) being but loose the chance to have it done by an algorithm that is reliable in a well documented way.
It would however be nice to have some indication that a pin represents more than one pad. (Maybe even indicate the number of pads it represents. Plus some way to discover which ones.)