One of my first clients every year knows they will owe the 2210 penalty and want to file the return and pay the tax as soon as possible to prevent a higher amount.  (Half their income is from CGD's in December, so the penalty using the annualized method is minimal and tax during the year is difficult to estimate.)  One year I did a manual 2210 and filed it with a paper return -- IRS ignored it and it took months to straighten the mess out.    

The problem is that Intuit programmers (like IRS programmers) are not return preparers.  They never have to consider the needs of real people.  

The 2210 and 2210 instructions are final, from IRS.  The delay is Intuit's choice.