hook_form_commerce_checkout_form_checkout_alter() changes are not reflecting on checkout page
Should it not be that the arguments are passed by reference?
You are not returning anything, therefore any changes you make within the function will have no affect outside it's scope.

function MYMODULE_form_commerce_checkout_form_checkout_alter(&amp;$form, &amp;$form_state, $form_id){
....
}