This is a weird one. It's a bug, I don't really expect anyone to be able to help but I'm posting on the off chance someone can direct me to the right place to look and/or have any advice for determining the problem. Or if by some crazy coincidence this is happening to someone else.
So after a bit of frustration I narrowed down the bug to this: dead Storm Atronachs (or any other large bodied Atronach) will prevent me from saving my game. This includes all save - manual, quick, and auto (discovered this when trying to leave Bleak Falls Barrow and got an infinite load screen). I can save mid summon, but after the creature disappears, trying to save freezes the game.
The next problem is that I'm having a hard time reproducing this. Creating a new game and summoning an Atronach (via god mode and unlocking all spells in the console) doesn't cause the same issue. Going through my mods (full mod list below) and deactivating/activating anything that might be linked to Atronachs/Spells/Effects/Lighting/etc doesn't produce any different results. I'm using the new SKSE64 Alpha which might be the problem, but I don't want to improperly report a bug if it's not whats causing the issue.
So yeah, if anyone has any ideas as to where to even begin looking, I'm willing to do the digging if you point me in a direction.