They have no way to do the same thing with Skyrim.esm so there are still unsolved mysteries about its contents.

The TES5Edit team reverse engineers the ESP file format by making changes in the CK and then seeing what it changes in the plugins.

The CK won't let you edit Skyrim.esm and there are record types and options in it that don't appear anywhere else. It's likely that their original version can edit some of the records we can't but it's also entirely possible that certain core elements in Skyrim.esm are generated and inserted directly into it by the game programmers to ensure that critical features don't get altered by the level designers and others that add content through the CK. It gets altered and certain features stripped out before we get it. The CK we use isn't the same as the one Bethesda uses. The very fact that Skyrim.esm unexpectedly changed size is your clue that it isn't like the others and you are headed down a bad path. We don't mod Skyrim.esm because we don't have any tools that can do so safely and because it's bad development practice that would ultimately lead to far more problems that it would solve. The special things they do add (for example, Dawnguard adding Vampire Lord and Werewolf Perk Trees) seem to actually be tied to the Engine somehow- even if you don't have Dawnguard.esm in your Data fold, you can still view the (empty) Vampire Skill Tree, which you cannot do for any non Skill-tree Actor Values. esm/.esp presumably there is some hard-coded links within the engine itself to Skyrim.esm to make certain things work (for example, somehow Skyrim.esm can contain Perk Trees/Skills, but we cannot make them-even if we duplicate and edit them, the best we get is nothing most likely the Engine directly references those Forms somehow.) There are like a dozen-or-so Forms hardcoded, but everything else comes from a. Skyrim.esm effectively 'is' the game-go move it somewhere, and try to load up the main menu: it CTDs after the splash screen.

How to use tes5edit to view conflicts