Also, what is the main difference between invalid packages and packages with skipped files? I cannot remember which one applies to Visually Enchanted Customizer Fixed which has ESPs at the top level and in a subfolder. It is invalid, right?
Invalid packages cannot be installed at all. BAIN doesn't recognize their general structure.
Packages with skipped files can be installed, but some files/directories won't be. BAIN either partially recognizes the structure (as with the mod you posted), or explicitly skips a file/directory that it refuses to install.
Technically, the mod you posted isn't invalid. Though it is in pretty awful shape for BAIN to handle.
Invalid packages don't have any recognized files in either the top directory or a package directory. If there is only one package directory, BAIN treats it as a special case and displays the installer as if it was simple.
Recognized files include:
masterlist.txt, dlclist.txt, *.esp, *.esm, *.bsa
Directories are skipped if the top level directory within a package directory doesn't match one of the following:
'screenshots'
'bash patches'
'distantlod'
'docs'
'facegen'
'fonts'
'menus'
'meshes'
'music'
'shaders'
'sound'
'textures'
'trees'
'video'
'streamline'
'_tejon'
'ini tweaks'
'scripts'
Also the directory is skipped if it matches:
'bash'
'obse'
'replacers'
Files are skipped if they match:
'.dll'
'.dlx'
'.exe'
'.py'
'.pyc'
'.7z'
'.zip'
'.rar'
'.db'
For this particular mod, BAIN tries to treat it as a simple mod because it has a single top level directory "Visually Enchanted Customizer-Fixed".
It finds esp files in that directory, so the archive is valid. It finds a top level directory within "Visually Enchanted Customizer-Fixed" that it doesn't recognize ("recolored shaders") so it skips that entire directory. Because it finds this extra directory, it labels the whole thing as a simple/complex archive.