I've been keeping up on the Fallout 4 modding scene in the aftermath of the update and a few more discoveries have been made.
Alongside the New FO4 update the CK got a update too, this update for the CK brings along a new version of the BA2 file type. (BA2 is a pack file sorta like a zip or rar but its only for CK engine games.) This new BA2 version is not backwards compatible with older versions of Fallout 4, meaning if you stay behind a version new mods will not work for you. However the new version of FO4 is backwards compatible with old BA2 files, meaning it should, in theory, load mod BA2s just fine. No one's really said what is or isn't broken yet in regards to mods, the new update seemed to mess with retexture mods, and I had issues getting certain model replacer mods to load but others work fine, but there isn't a big list of what will and won't work yet.