Drupal 7 Webform - Find input regardless of fieldset
Unfortunately, to access/modify and form fields in Webform using the form API and hooks, you have to know/include the fieldset hierarchies in the array calls as you observed.

For example:

$form['submitted']["fieldset_machine_name"]["certain_name"]


or

$form['submitted']["outer_fieldset_machine_name"]["inner_fieldset_machine_name"]["certain_name"]


Rather than set a callback function on the form element in your hook_form_alter, you may just need to find the element type with particular machine name using vanilla javascript or jQuery in either:


your theme's assorted javascript files as Drupal behavior
the custom module as a separate script