I've read this in a couple places now and I can't reconcile it with the behavior described here. Quoting part of it:
Note that this applies to enchantments as well.
A consequence of this is that, if you modify the base cost of a magic effect, then in order for that base cost change to take effect on autocalculated spells and enchantments that reference it, you must touch that record in your mod, even if you don't intend to make any changes to that spell or enchantment. For example if I want to cut the magicka cost of the Flames spell by half, then I must change the base cost of the magic effect, but I must also copy in an ITM of the Flames spell into my mod, so that the game will recalculate the cost when it loads my mod. If I don't, then while my change to the magic effect will be loaded into the game, the effect of that change will not be reflected in Flames. (It will be reflected in spells loaded after my mod, if they use that same effect.)
I suppose the answer might be "the auto-calculated cost of the spell or enchantment will be reflected on the spell or enchantment entry in your mod." Except, the game doesn't do anything with that. There is no reason to change it, and it's a pain in the ass to cycle through each of them in the CK just to update a value that will anyway be ignored when starting up the game.
I would like to be wrong here! I have a mod that does something like this, except with enchantments, and if there is a different, better thing I should be doing instead, I'm all ears.