@MisfitBec Custom content and script mods are two separate settings under Options > Game Options > Other. "Enable custom conten and mods" refers to .package files, which covers all cc and also .package-based mods; "Script mods allowed" refers to .ts4script files. So you can mostly accomplish what you want, but you'll need to be careful about mods that include a .package element still affecting your game.
In your position, I'd sort my mods and cc into subfolders and simply remove the one(s) that might be a problem post-patch. Script mods can be one subfolder deep, i.e. Mods > folder name > pile of mods.