Propose Directory Structure

At public/index.php you have a call to the app folder (for Config/Paths.php) this path must be set correctly to your app folder (for each separate public folder there should be selected APP folder it can goes automatic but I don't recommend it).
! This should be the only place where the system is not using those Paths.php folders paths, so don't forget to update and folder names inside this Config/Paths.php. after that !

for .env file I am not quite sure .. I think it's hard set to the root folder :/ May be it should be possible to set its path inside config paths as well ? ? ?

If the directory structure that I propose is approved, we only need to update the basepath definition in system / bootstrap.php.