I don't think the IRS is going to return penalty funds that they have already collected. If you had known, you could have asked about the abatement earlier, but that's water under the bridge at this point.
It's also worth noting that if you owed tax, you also owed interest, and that can't be abated even if the penalty is abated. If the penalty is reduced or eliminated, the interest will be recalculated to cover just the tax, but you would still owe the interest. At this point, if they cleared your remaining balance (which included some percentage of tax, interest, and penalties) that's a pretty good result. You would have to recalculate your entire payment plan from the beginning with tax due and interest but no penalty, to see if you are really losing anything. It's always possible that they will do this automatically. And there is no harm in writing a letter explaining your argument, but you would need specific calculations showing how your payment would be applied to just the interest and taxes, to justify that you covered the amount owed.
