Any mods loaded with references to deleted records from the Official Bethesda DLC will cause your game to crash. The Second reason is that Bethesda chose to delete some things that are in the Official DLC. Chance is remote that a master will affect another master, and this procedure is best used on all of your mods plugins, but cleaning everything of ITMs ( Identical to Master records ) causes no harm, is more optimal giving the game less to process in your load order, and so it is best to get rid of these completely unnecessary dirty edits. The masters are very early in your load order but there is potential for a mod to be made as a fake.esm, and placed among them, and so ITMs in a later loading master may cause problems for that mods esm. Which can alter mods that you have for Weapon Damage, Armor, Lighting, Food Effects and so on.

It won't cause crashes, it just changes the values of plugins loaded before it. Wherever that plugin is placed in your load order its records overwrite all the conflicting records from plugins loaded before it ( the rule of one ) resetting the settings back to the values contained in the Official Bethesda DLC. The Official Creation Kits are notoriously buggy and randomly create dirty / wild edits, often when the author of the plugin is completely unaware.

They exist because Bethesda may have looked at something in the CK and an unneeded entry was auto included in the plugin even though the item was not altered in any way. Firstly because the masters have entries that are identical to the same records in Skyrim.esm or other DLC esms'.

Save game cleaner skyrim sse