folder structure Plugin.vst3\Contents\x86_64-win\Contents\Plugin.vst3

What is the use of the folder structure

Plugin.vst3\Contents\x86_64-win\Contents\Plugin.vst3
Plugin.vst3\Contents\Resources\PluginGUI.uidesc
Plugin.vst3\desktop.ini
Plugin.vst3\PlugIn.ico

if everything works with the single file Plugin.vst3 ???

check the doc: https://developer.steinberg.help/display/VST/Plug-in+Format+Structure