There are two different penalties involved. The first is "Underpayment of Estimated Tax by individuals" penalty and the other is the "Failure to pay" Penalty. The underpayment penalty can be avoided by paying an amount equal to 100% of the prior year tax (or 110% if AGI is over 150K).
However the failure to pay penalty applies when taxes shown or required to be shown on the annual tax return are not paid by the due date.
So if with the extension form 4868 the taxpayer pays enough taxes to meet the 100% (or 110% as applicable) of last year's tax amount then the underpayment penalty is waived. However, if the amount paid by the due date (18 Apr for example) does not cover the taxes reported or required to be reported on the tax return then a failure to pay penalty applies.
Here is a list of penalties for reference.
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