This function purpose is to simply avoid other mutators from replacing something you actually want to keep.
Let's say, for example, that you have a weapon mod which replaces every weapon in the game, but there's one particular weapon you don't want to be replaced at all, so you can build a mutator which tells the game that you want to keep that weapon, therefore the weapon mod won't be able to replace it.
Having that said, some weapon mods allow you to disable certain replacements from happening from their .ini files, thus you don't really need to implement this in those cases.
However, it's generally best to abstain from using this, given that if a mod wants to replace something, you should let it replace it unless you fully understand the full repercussions of it, or not use such mod at all.
Let's say a mutator actually needs to replace item X otherwise it won't work properly, and then you come along and use AlwaysKeep to prevent it, then you have pretty much broken the other mod.
On the other hand, let's say that a mod does replace item X by another, but this new item is broken in some sense, but not the rest, you can use AlwaysKeep to keep that item unreplaced avoiding the problem altogether, and still enjoy the rest of the mod.
In other words, it's the kind of function where you have to understand the implications towards other mods, and should only be used if you have a really good reason to.