ChemBoy1

The extension is not packaged correctly. There should be no folder above the index.js and info.json files. The author needs to remove that folder and re-upload a new version of the extension. There is already a bug report on the mod page about this. Perhaps @Pickysaurus or another moderator needs to correct this if the author is no longer active in the community.
 
https://www.nexusmods.com/site/mods/516?tab=bugs

The lack of NTFS formatting is definitely the issue. Was just talking with another user here on the forum that had a similar setup with an external drive not formatted in NTFS. 
I would highly recommend reformatting your external drive. if you have drive laying around you can backup your files, reformat the drive, then copy the files back to it. 

You need to enable the "Enable Profile Management" setting. 
 

If you are getting corrupted save game files, that suggests a hardware failure. Skyrim won't give you a corruption message for missing mods. Corruption message means the actual save file was damaged. Missing mods just give a warning before loading the save and may lead to crashes if critical mod data is missing. 

Make sure you are downloading from the correct site for your game (Skyrim vs Skyrim SE).
 
You have to be managing the game for the mod you're downloading or you will get the prompt. This is by design.

@Mortasi - This is happening because an installer for another game extension in Vortex is "hijacking" the installer. This happens when the extension author does not properly check the game ID when testing if the installer should be used.
What 3rd party game extensions do you have installed? The culprit would be an extension for an Unreal Engine based game

Yes, the blue banner is just letting you know there is no metadata, but there never was before the update either. That is why it is not an issue and is purely cosmetic. LOOT cannot sort plugins with no metadata anyway. 

So the thing you need is the function call to the "RequiresLauncher" function in the registerGame function:
requiresLauncher: makeRequiresLauncher(context.api, gameSpec),  
If you are not using the "Add Game Wizard" structure, you can literally just skip the function call and write this: 
requiresLauncher: () => { launcher: 'steam' }, This should work in this case since steam launcher requires no additional parameters to function. If it were Epic or Xbox app, you would need to have additional parameters there.
 
You also need to have the "findGame" function return an arrow function to the value, like below. Notice the arrow function after "return".
function makeFindGame(api, gameSpec) {     return () => util.GameStoreHelper.findByAppId(gameSpec.discovery.ids)         //.catch(() => util.GameStoreHelper.findByName(gameSpec.discovery.names))         .then((game) => game.gamePath); }