TW3MM has integrated merging functions (KDiff) for scripts that need to contain lines of code from different mod sources, which is pretty common when you start running a hundred mods. You can also selectively delete the compiled script merges that you make and re-merge them if you have issues in the script manager, which by itself would be enough reason to use TW3MM over Vortex. If the automerge causes a problem with compiling, it will tell you which file, so you can delete the automerge and selectively choose which of the two or three (or combination and order) of the mod script lines you need. TW3MM also supports prioritizing mod loading order, so things will be loaded in order and may prevent the need for some messy merging or file version selection. It also keeps a list of data files in your DLC folder, many of which are needed by mods in the Mods folder, which is what TW3MM primarily handles. There are some mods that need to be manually unzipped because they modify files in the bin folder, but I can count on one hand the number of these I use out of over 100 active mods. The only other piece of the puzzle is your My Documents/The Witcher 3 folder that contains input.settings, containing key bindings that some mods need. Here's a full installation guide for running The Witcher 3 with the full baseline of community patching as of March 2021