Is it possible to bypass form validation, but still save form data?
The solution dawned on me this morning; to get this functionality in place I need to work backwards: rather than having Drupal validate the required fields and conditionally disabling the validation, we should remove the validation requirements from the form, and conditionally add them (doing custom validation, if need be).

So, the #required parameter is set to FALSE for all fields, and a custom validation handler conditionally checks the 'required functionality.'