It won't. There are too many different ways to measure progress. Plus, you do not put Story Point estimates on sub-tasks.
It allows you to have story points at both levels even at same time.
customer is demanding points and effort at sub task level plus points at story level for dev team motivation purposes even though they know its double counting
we need Atlassian to confirm when this enhanced functionality might become available
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It allows you to do that if you want, and your customers can demand all they want, but if you estimate story points on sub-tasks, your burn-down charts and velocity all fail. So you shouldn't do it.
Atlassian have no intention of changing this at the moment (and hence, no intention of doing completion percentages)
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Burn down appears to just reflect story level so should remain consistent as per stakeholders requirement but I will double check
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