Yeah, I agree, it is quite annoying.

If I remember correctly, it is just for underpayments when uneven Estimated Tax were paid (probably the 'regular'/annualized method on the bottom of the form).  Or something like that.

If the penalty is only a couple of dollars or so, I 'cheat' and change the numbers to get rid of the penalty (and tell the client they could get a bill in the mail).  But I wouldn't do that for a penalty that large.