ChemBoy1

The "Plugins" Load Order tab in Vortex is for sorting the load order of game engine data plugins (.esp, .esm, .esl). The "plugins" for SKSE are .dll files. So these are referring to different things. There is no load ordering for SKSE .dll plugins. If the .dll files are present, they will be loaded by SKSE.
Make sure you have LOOT enabled in the Load Order tab to auto-sort and enable plugins.
Read the mod description for the mods you are using to see if SKSE is required for that specific mod. 

Hey there. I am the author of the SOTTR Vortex extension. You need to run the SOTTR Mod Manager tool in Vortex after installing mods to actually apply them to the game files. The mod files are installed in that "mods" folder.
Can you be more specific about the error messages you are seeing?
Can you follow this guide and let me know the Epic Games ID (AppName)? I also need to confirm the name of the game executable. This will ensure that we can launch the game properly from Vortex and automatically discover the install location.

Library Information for Epic Games Store and Steam | Jayden’s Blog

Did you previously have the GamePass version of the game managed in Vortex? If so, you need to "Stop Managing" the game and then add it again. 

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 Perhaps @Pickysaurus or another moderator needs to correct this if the author is no longer active in the community.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); }