Is there a way to run hook_form_alter after themes implementation?
I think you cannot have a module hook executed the same hook implemented by a theme. If we look at the hook invoking code, we see that the theme hooks are invoked separately and after the module hooks.

The best bet would be to remove it from the theme and put it in a module, or trying with #after_build.

FormBuilder.php contains the following code.

$this-&gt;moduleHandler-&gt;alter($hooks, $form, $form_state, $form_id);
$this-&gt;themeManager-&gt;alter($hooks, $form, $form_state, $form_id);