How to pass a form field value from THEME_system_theme_settings_alter() to THEME_form_system_theme_settings_submit()
The answer to the question is quite simple, but not easy to find in the d.o. docs. Thanks to Clive and Jack-PL who gave me the right direction. To reuse the example from the start question we need to summarize:

A form field input value needs to get splitt off (intercepted) from its usual way getting stored for a short moment. Why? For us to do our own processing while submission before theme-settings.php Party is over. Our form field:

// theme-settings.php
function THEME_form_system_theme_settings_alter(&amp;$form, &amp;$form_state) {
// Test form      
$form['whatever_fieldset_group']['user_input'] = array(
    '#type' =&gt; 'textfield',
    '#title' =&gt; t('Test to get value'),
    '#default_value' =&gt; theme_get_setting('user_input'),
    '#description' =&gt; t('
         Type some text in textfield 
         to get shown in submit message'),
);
}


Now the value will get stored when the user hits submit button. But what if we need to get in between before?

Injecting ...

drupal_set_message('&lt;pre&gt;' . print_r($form_state['input'],1));


... in function THEME_form_system_theme_settings_submit for a moment has revealed, that we were looking for $form_state['input']['user_input'], were our fruits are hanging. Searching the value with drupal_set_message('&lt;pre&gt;' . print_r($form_state['input'],1)); gives us orientation to be able to intercept the right value for our own value processing, demonstrated here in a simple representational form with another little drupal_set_message() scenario:

// theme-settings.php
function THEME_form_system_theme_settings_submit($form, &amp;$form_state) {

    // the following will not work inside theme-settings.php
    // because value is not known yet by theme_get_setting()
    // $data = theme_get_setting('user_input');

    // But this works!
    $data = $form_state['input']['user_input'];

    drupal_set_message(
          'For testing purposes we submit that you have 
           filled the textfield with the following 
           mindless value: '. $data
          );
}


In my case, I was able to save user input into a file now with file_unmanaged_save_data($form_state['input']['user_input'],$filepath); while the user hits submit.

Thanks to Clive and Jack-PL for the fast reply. It helped me a lot!