There are lots of reasons why it is bad to be over-withheld, beyond losing out on interest.
I think we've all learned the risks of catastrophe impacting our government's ability to carry out business on a timely fashion, for one.
It is much much better to make an estimated payment.
From a tax professional standpoint, the problem is that so many people who SHOULD be making estimated payments forget to, or when they have their return prepared, can't pull the records to remember what they did if they did.
One solution a professional can offer is to set up automatic payments upon filing of the return, but that's a one shot deal to get it done. It then falls on the taxpayer to remember to have sufficient funds in the account on the withdrawal date. The scheduled payment can be cancelled or altered after filing, but it takes a phone call to IRS to do it, and you can imagine why anyone would want to avoid that if at all possible.
By and large though, if someone's income is through regular periodic payments such as wages, retirement, or social security, they should be using normal withholding and not estimates.