Straight to the point: an item which has been ReserveItem()ed by a script, shouldn't still be able to be accessed by the same script through core API? I mean, for example, FindSubstance(), this is its actual behaviour

FindSubstance(... some item) -> return array of 1 item
ReserveItem(array[1]) -> correctly returns 1
FindSubstance(... some item) -> return error{ errortext = "Not enough of that substance in container" }

technically yes but technically no... the question I have for you is why would you have to FindSubstance on an item that you already found and have a reference to?