What does you may elect to treat the tax withheld as paid when it was actually withheld mean?

If tax is withheld from the income you receive it is considered paid.

That is still very confusing. Based on this wording, wouldn't it always be in our best interest to select "yes"? For figuring underpayment penalty, in what circumstance would we not want to consider withholding as payments?

At the screen Actual Withholding, it states:

 

The IRS treats your total federal income tax withholding (from wages, interest, dividends, gambling winnings, etc.) as being paid in four equal quarterly installments.

For purposes of figuring the underpayment penalty, you may elect to treat the tax withheld as paid when it was actually withheld.  Would you like to do this?

 

In many cases you would say "Yes".  However, if a large amount of income is earned with no corresponding tax withheld very late in the year, the four equal quarterly installments of taxes that were withheld may better offset the income reported.  You may want to compute both ways.

 

@MaxLohMusic