IRS: Does FBAR reporting apply to offshore accounts if the $10,000 threshold was met only briefly within the same day, without remaining overnight?

Yes, if the aggregate value exceeds US$ 10,000 per year, an FBAR report has to be filed by the bank. Its irrespective if the amount stays in your account overnight, short term (day transaction) or long-term. If the amount is breached as a transaction for your account, it would be reported.