Option A is the only legal alternative.
The tax court has ruled that Form 5329 is considered to be a separate tax return, so the statute of limitations on the IRS assessing the excess contribution penalties for 2014 through 2016 does not start to run until you file Forms 5329 for those years. Additionally, since the excess is subject to penalty each year the excess remains in your Roth IRAs, so your 2017 Form 5329 should be showing $6,900 on line 18, carried forward from line 24 of your 2016 Form 5329. Omitting that would be fraudulent.
The penalties calculated on your 2014 through 2016 Forms 5329 will be $690, not just "a few $100."
