Drupal and its modules kept in two different subfolders -- possible/how?
install it with the core and the modules kept in separate folders, rather than in a hierarchy


In short, no.

Drupal must be able to expect to find files in a certain location, and that is not dynamically configurable. The very first line of code Drupal executes is define('DRUPAL_ROOT', getcwd());, and file wise, most things are based on that constant.

Symfony, and PSR-0, doesn't inherently change that. PSR-0 only defines the directory structure around files, not where to find them. With that said, I haven't looked in enough detail at D8 to know if there's a simple way to alter where the autoloader looks for files.

If your filesystem (and webserver) supports symlinks, you can work around the problem by symlinking the appropriate directories in place.