There are two types of 'clean saves'. One is actually a vanilla save, the other is a bad modding practice in an attempt to re-initialize a badly scripted mod or an updated mod that doesn't use version control to initialize its scripting when a user updates. Or the modder doesn't understand about persistence and doesn't realize that you cannot update some mods in the middle of a game.
Vanilla save/Clean Save
No mods enabled.
Also known as re-initializing a mod and is only used if a badly scripted mod stops working or a mod author has not included version control scripts to reinitialize quests and scripting.
It is not advised on any platform to disable a mod and continue on the same save. Due to persistence and other issues, most scripted mods cannot be updated in the middle of a game.
Levels of Persistence - Mostly Skyrim related but contains information about Fallout 4 as well.
Creation Kit Technical Information: Save File Notes