Withholding credits are not considered paid on 12/31.  Think about it, the employer may not have to pay them until 1/31 of the following year.  What the law says is that they are considered paid on 4/15.

"Even though it is "whichever period expires later," what does that mean when a return was never filed?"

But we are not talking about a return never being filed.  We are talking about a return being filed at the same time the statute is about to expire.