Is washing with water during Istinja' similar to Istijmar in that it does not require 100% purification of the area, and pardon in it is considered permissible, in order to save time and water?

Cleansing with water (Istinja') involves thoroughly purifying the area and completely removing the impurity itself until it returns to its original state before the impurity. As for cleansing with stones (Istijmar), the remaining trace that cannot be removed except with water is overlooked. There is no need for exaggeration in cleansing; if you are certain or highly confident that you have purified the area, then you should proceed.