Best Practices for altering forms.

I've recently learned the difference between altering a form through a theme hook, such as mytheme_form_id($form) in template.php (...which changes the look of the form, but it doens't change the functionality...so when I unset($form['some_required_field']), it was still a required field and it would not let me submit the form....enter hook_form_alter)

And, changing a form using a hook_form_FORM_ID_alter(&$form, &$form_state) in a module. (...which passes the form and form state by reference so that changes will save before being handed off to themeing functions....therefore, if we unset($form['some_required_field']), then drupal will not be expecting it and the form will work correctly.)

My Question: If I've got a few different sites on a mutlisite installation, which use different themes and require different form stylings. Do I just create a module for each domain....and in each module, have a list of 6-7 hook_form_FORM_ID_alter functions? ... I just feel like I'm writing a hack, and that there must be a better way to manage my custom forms.

Thanks