Good reason to pay online.  Did the credit union give him a copy of the front and back of the check?  That will help IRS find where the payment was applied.  Were his SSN and tax period written on the check?  If not, and the check was separated from the voucher, IRS would have to use the "unidentified remittance" function of its primitive computer terminals to track it down.  

"Apparently the IRS is now using scanners" -- come on now, you know better than that.  The banks that IRS has hired as private contractors for their "lockbox" operation, might be using scanners.  Someone has to feed the scanners, of course, but those aren't IRS employees.  This work was farmed out decades ago, to make it look like federal government employment was shrinking.  Some jobs, like handling tax collection, really should be left to government employees.  Look at the problems that faced Putin, when he hired private mercenary groups to fight his wars in Ukraine and Africa.