So, I'm using this version of Security Craft for 1.12.2 (https://www.curseforge.com/minecraft/mc-mods/security-craft/files/3577171) and the latest version of Aether 2 crashes when any mod that loads Mixen into the game is added. I would use the other version of Security Craft (https://www.curseforge.com/minecraft/mc-mods/security-craft/files/3577164) but my game crashes with that one as well and it is completely unrelated to the problem I'm having now.

Just using The Aether II and the no-mixin version of SecurityCraft does not crash my game. Please always include the corresponding crash report when you report a crash.
In any case, The Aether II uses Mixin 0.7, while SecurityCraft needs to use Mixin 0.8. As a result, SecurityCraft's mixins will not be loaded when The Aether II is installed. This can easily be fixed by installing the following mod alongside the no-mixin version of SecurityCraft: https://www.curseforge.com/minecraft/mc-mods/mixin-0-7-0-8-compatibility