How is this realised? When we implement, for example, theme_preprocess_page(&amp;$vars) function, we can alter variable that are visible as not array items. 

What I mean: $vars['somevalue'] from theme_preprocess_page(&amp;$vars) function is further  available in page.tpl.php as $somevalue. How is it possible? Definitely there is some kind of automatic generation of variables but the implementation is unclear.
Clive's answer is correct. I am just pointing out where exactly that happens.

theme_render_template() is the function called by theme(), and it contains the following code.

  extract($variables, EXTR_SKIP); // Extract the variables to a local namespace
  ob_start(); // Start output buffering
  include DRUPAL_ROOT . '/' . $template_file; // Include the template file
  return ob_get_clean(); // End buffering and return its contents


The code that calls theme_render_template() is the following one.

    // Default render function and extension.
    $render_function = 'theme_render_template';
    $extension = '.tpl.php';

    // The theme engine may use a different extension and a different renderer.
    global $theme_engine;
    if (isset($theme_engine)) {
      if ($info['type'] != 'module') {
        if (function_exists($theme_engine . '_render_template')) {
          $render_function = $theme_engine . '_render_template';
        }
        $extension_function = $theme_engine . '_extension';
        if (function_exists($extension_function)) {
          $extension = $extension_function();
        }
      }
    }

    // In some cases, a template implementation may not have had
    // template_preprocess() run (for example, if the default implementation is
    // a function, but a template overrides that default implementation). In
    // these cases, a template should still be able to expect to have access to
    // the variables provided by template_preprocess(), so we add them here if
    // they don't already exist. We don't want to run template_preprocess()
    // twice (it would be inefficient and mess up zebra striping), so we use the
    // 'directory' variable to determine if it has already run, which while not
    // completely intuitive, is reasonably safe, and allows us to save on the
    // overhead of adding some new variable to track that.
    if (!isset($variables['directory'])) {
      $default_template_variables = array();
      template_preprocess($default_template_variables, $hook);
      $variables += $default_template_variables;
    }

    // Render the output using the template file.
    $template_file = $info['template'] . $extension;
    if (isset($info['path'])) {
      $template_file = $info['path'] . '/' . $template_file;
    }
    $output = $render_function($template_file, $variables);
  }