Is there a option to install plugins unattended? Using command line?

No. Other than manually (or using a script) copying DLLs and files into the appropriate location…which is all the PluginManager does.

Even setting allowAppDataPlugins.xml some files still needed to put into main directory under Program Files

This is true although the majority of plugins are perfectly fine using the app data directory.

Or should we grant rights for users to NPP main dir?

That’s completely up to you.

It will be a high level layer calling the existing underlying layer. That layer will not go away.

Please supply more information on what changes needs be done for fixing bugs as you hint .