Your mod sounds very interesting, but unfortunately I've never looked much into traps and so I can't be of much help there.
It might help to know what's exactly causing the problem. Do area effect spells work at all when targeted on the player? I've never seen NPCs casting them, so I don't know. Or is it "just" a problem of traps? Also, there is currently no active development on the Code Patch, so if you're looking for a quick solution, it might be better to script around the bug. (You could determine the distance between player and trap and add the trap spell's effect to the player if he's near enough).
1.
You have seen area effect spells, I think. Daedroth creature use area effect poison spells and they work correctly, so it's a bug for the traps only.
When you set off trap, it shows effect, but do not deal any damage with it if you used Telekinesis.
For your scripting workaround.
It can be a great workaround for modders who add one or two containers with traps, but scripting hundreds of in-game containers and doors with traps will not be a very good solution, I'm afraid.
Really, I'm not looking for a fast solution, because the project is massive (much better than "UUMPP" rival project, I hope) and still needs a plenty of time.
2.
Another bug is not a bug at all, but a suggestion. As you may know, most players use quick workaround for all speechcraft, mercantile, alchemy, enchanting and sneak skill requirements. For example, to create great potion you do not need any alchemy skill. Just create "Fortify Alchemy" spell with 100 magnitude for 1 second. It will cost 5 mana! Cast it and make your super-potion. With 5 mana points cost, the spell is available even for novice, thus ruining all game balance. "1-second" spells is really like an in-game cheat.
So, my suggestion is to limit all "fortify","invisibility","telekinesis" and all other player-improving spells to have at least 10 seconds of duration. It will not change anything in the game data, because "in-game spells"(not created by player) already have at least 10 seconds duration by default, so it will affect only "spellmaking". With this limitation, you will need 50 mana and a high restoration skill to make 100 magnitude "Fortify" spell.
Is there a way to implement this? You have changed maximum magnitude, so there must be a way to change minimum duration. What do you think? B)