Same errors with ModKit 1.3 and patched / unpatched wcc_lite. Everytime I tried to uncook or extract the game or even just one mod, wcc_lite.exe crashed with 'Assertion failed' errors (like when trying to extract HQFaces Mod bundles as shown here (pastebin) ).
Encountering of course the famous mod limit for textures and mods in general I researched ways to bypass this and found some tips and tutorials for this involving the official ModKit 1.3 (guides for using wcc_lite with command line, GUIs like Mod Merger or the great tool in development WolvenKit, this post by Lim3er0 etc.), but everything didn't seem to work for me. A few days back I decided to play The Witcher 3 for the sixth time (first time in two years) and wanted to try various mods I haven't tried before (textures and quality-of-life stuff).