Like I said, it is possible that Itachi and Sasuke simply needed a very quick easy way to free themselves and so they used the most available option. It is possible that they could have bitten tougues, broken fingers, stopped their chakra flow, etc. Yet those methods would not have been as quick so they just did what was quickest and caused the least amount of damage to themselves. Yet, my problem still remains, we haven't been given any sort of explanation for different types of genjutsu requiring different counters. It makes it confusing.