zftool is primarly a module for zf2 app. If you want to use zftool, you can install it into `vendor/` and it will provide routes/functionality within your app. 

I haven't ever renamed my console entry point the way you describe it. I usually leave the default one (which amounts to something like `zf` or `drush` in drupal, or something else), or call it `./shell`. 

This means I usually end up having:
 `/some/path/FooApplication/shell --do --something` 
which is more logical to me than what you propose:
 `/some/path/FooApplication/bin/FooApplication --do --something`