custom multiple values form element
Is there a way to convince drupal to take in into $form_state['values']


Yes...use the Form API :)

To expand; Drupal builds and caches the fields for a form on the server side, and uses that cache upon submission to make sure the form hasn't been altered. Drupal, rightly, sees the injection of arbitrary HTML into the structured form as an attack vector, a security hole which must be plugged up.

Consider what would happen if this weren't the case - a client using your form could inject some HTML form values, overriding your particular intentions for the form submission. As Drupal cannot possibly reconcile the context in which that HTML string was added, it has no way to know if it's come from a trustworthy source.

Bottom line - if you want to add a field to a form that's managed by the form API, your code absolutely needs to conform to the same API - the alternative is to fight against it, which is never fun.

It's physically possible to get around the validation, but the amount of time it would take to convince Drupal to accept your injected form values, and at the same time keep it secure, would far outweigh how long it would take to use the form API as it was intended.