It's a mod organizer like all the others but it has a functionality called "bashed patch" which can combine simpler mods or, what you've heard, the "leveled lists" included in said mods. I don't understand exactly how that all works yet, as some mods definitely show up without merging their leveled lists, but it's a reasonable thing to do if you have a bunch of equipment mods and want to make sure said equipment shows up in the hands of enemies, in chests and available for sale from merchants.
It's easy to do. Just install and open Wrye Bash and create a patch, opt to skip merging mods unless you're sure that's what you want to do and hit the "leveled lists" section. It should automatically fetch mods that have "bash tags", but not every mod has them. For example, I have Lost Library and it does not have them and needs to be added manually. Manually add all mods that you think have leveled lists (if they don't, nothing bad will happen as far as I know, Wrye Bash will simply add nothing from those mods to the patch) and hit "build patch". There are several youtube videos on this. (Though, strangely, Gopher seems to refuse to make one...)
That warning means that you've uninstalled a mod that you were using previously, as Skyrim includes content from mods in your savegame.
T5E is not a savegame cleaner, but
this tool is. When you open a save with script remnants from disabled mods, it will say "X orphaned scripts found" or something to that effect. Hit the "FixScriptInstances" button to clear those. Then enter a # into the Scripts search box in the top left to filter only scripts marked with a # (which also means remnant left by uninstalled mod), then expand the tree below the search box to make sure the scripts being removed are from mods you want to remove. They will most often have logical names like everything belonging to for example Wearable Lanterns will start with a "WL_" prefix. After making sure, hit "Delete all #".
If you have no idea what mods you've removed and don't know if it's safe to clean your scripts... Well, you've just learned your lesson not to haphazardly install and remove mods. Messing around like this without paying attention will break your save sooner or later.