If you file the extension request using Form 4868 then nothing is sent to the IRS concerning any tax refund. Only the 6 month extension for filing the actual tax return is being requested with the Form 4868.
It is your choice, you can file the tax return now and get any refund shown on your filing and then file an amended tax return when you have all your documents. Or you can wait until you have all of your documents and file your complete tax return at a later date.
Note - If you are going to be receiving a tax refund with your completed filing there is no need to file for an extension. There is no penalty for filing a tax return after the due date if the tax return being filed has a tax refund. You have up to three years from the original due date of the return to file for a tax refund. For tax year 2016 that would be on or before April 15, 2020.
