Consider the following...
You have partially competed the return and are confident that you will be getting a refund, but you decide to not file a return/extension request by April 15th, and just submit the forms when you have all the missing information.
The problem is that 1099s and W-2s connected to you have been sent to the IRS and state tax office. As some point after the deadline they will be attempting to determine if you should have filed a return. If the income they know about is over the required to file threshold they will be expecting a return.
The tax authority will then determine if you owe or are due a refund. While they do have income information, they might not have all the numbers that will reduce your income tax. They don't know about charitable contributions, they don't get IRA contribution info until May, they don't know about your property tax. So they take the safe route and assume that you are single and taking the standard deduction. Which means you might think that you are due a refund, but they disagree based on the numbers they have.
When will this catch up to you? I don't know. But to avoid the issue file for the extension, and estimate what you owe or the refund you are due. Don't leave it to the tax authorities.