It creates issues like leaving your game broken after uninstalling a mod (leaving an empty folder in your DLC which stops the saves from loading). https://www.twitch.tv/videos/416825592
Also, some mods require you to take extra steps i.e add a few lines in your input.settings file, Vortex can't do that. Vortex can also place a mod's files & folders in the wrong place.
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Also, some mods require you to take extra steps i.e add a few lines in your input.settings file, Vortex can't do that. Vortex can also place a mod's files & folders in the wrong place.