I'm a fellow user, not a tax expert, but I can tell you how that works.
The IRS calculates penalties for underpaid estimated taxes by quarter. Any overpayment or underpayment from a quarter's calculation are carried over into the next quarter and figured into the next quarter's calculation. If any one quarter is calculated as having an underpaid balance, there can be a penalty even if the total amount of estimated taxes during the year is enough to result in a tax refund on the 2021 return.
You could make a larger June payment to include April's payment to make up the difference and prevent penalties and interest for the first quarter from further accruing. That will at least stop a possible penalty and interest incurred from the first quarter from growing. But it will not "atone" for any possible penalty for that unpaid (late paid) first quarter. Paying extra above that (i.e., including the September payment in advance) won't help any further. But even paying April and June together won't prevent any underpayment penalty that could result from the first quarter's estimated taxes not being paid, but should stop it from growing. That will all be calculated by quarter on next year's tax return.
I am really sloppy about this. I usually roll most of my refund forward into next year's taxes. As long as one pays in at least the previous year's tax burden, anything paid by the Apr 15 deadline counts as good. So I make up any additional when I file an extension. They never bother with me. Just get enough money on account with them, and don't worry about it.