welcome in the community!
Login box doesn't require a file in tiki/modules/ "because" it's some kind of core function anyway.
The Smarty assignations apply to the whole script. If smarty is assigned the value of $user from tiki-setup_base.php or tiki-setup.php for example, then until it's assigned another value to $user, $user will stay defined even in the modules's templates.
BTW, make sure to come at IRC #tikiwiki, you could get answers (even!) faster.