You are able to file as married filing separate for 2016.
The statement that you are referring to (about not being able to choose to file separate returns after the due date of the return) means that you canot file a joint return for 2016 and then try to amend that return to married filing separate status if the amendment is done after April 18, 2017. This means that you are no longer able to amend your 2015 return to change your filing status to separate, but you are able to file your 2016 return using the separate status.
