Withholding has an advantage of estimated payments in that withholding is divided evenly throughout the whole year (unless you choose to do otherwise).
Estimated payments paid after the quarterly due date are moved into the next period.
What's the difference? You can increase your withholding later in the year and have it spread back to earlier periods, which you cannot do with estimates.
For example, suppose you owe $8,000 and made no payments until the last quarter. Your withholding would be averaged ($2,000 per quarter) so your withholding your cover your tax for each quarter.
The estimated payment would be credited to the last quarter meaning you would have underpayment penalties in quarters 1-3 because you paid $0 estimated tax in those periods.
