Interestingly as I work on a new overhaul of mine I might've learned something useful for future modders, or at least something I never heard or read about until a very frustrated day or two of messing with the Creation Kit. Take a look at this screenshot of something very simple in theory... http://imgur.com/a/KnE0PBoth use the exact same condition, only difference is one is a perk conditional the other is a spell conditional. Not a single thing I do makes the spell conditional work, yet my first attempt of trying an identical condition on a perk is nearly miraculous.

So... Is it just me or are there some things where spell conditionals will work for perks but not spells? Now maybe there's a tiny chance I'm confused about something, but I'm like 99% sure today even after years of modding, I learned the hard way some conditions only work on perks but not on spells... And maybe hopefully someone who is frustrated with the CK can be saved some hours of frustration by coming across this thread.

(When in the past I thought only some EFFECTS were limited to perks, but now I suspect some conditions are too).

Edit: (I even tested with an apply ghost visuals effect replacing the custom destruction spell just to be sure, and still only the conditionals on the perk work, further convincing me of this new Creation Kit theory).

There are multiple places you can use conditionals with spells and spell effects. The differences I've found indicate to me that the differences are related to when the checks are made and what they affect. But that doesn't mean that you haven't found something new here.