I dont' understand.
The only spaces in the paths and they are in "Witcher 3 Mods Tools" and "Witcher 3 Wild Hunt" and they are automatically during installation.
Does C:\users\username\.... still work the same on Windows 10? I thought I saw somewhere that they'd made big changes to it. Try saving it somewhere else, in a "real" location rather than a virtual one.
Old trick which is needed when handling command prompt/bat files
For paths which contain spaces you need to use quotation marks, so your paths would be:
-indir="D:\GOG\The Witcher 3 Wild Hunt\content"
and
-outdir="D:\Witcher3_Modding\Uncooked"