"There is no need to amend since nothing else on the tax return would change. You can submit the 5329 forms by themselves. You are amending anything since you never filed the 5329 forms in the first place, you are just filing the 5329 that should have been in the original tax returns late."
This is an absurd statement.
Of course something is different the tax owed is increased, due to the addition of Form 5329.
Use Form 1040-X to change or add information on an already filed tax return.
Since the penalties accrue through the years, I think one amended return with all the penalties would be accepted.
You will have to attach a detailed explanation since what you are doing won't fit in the Part III box provided.
You are able to request waiver of some or even all of the penalties.
See Form 5329 to request a waiver of the penalty.
You will have to pay the tax on the earnings and probably interest.
Meanwhile respond to the IRS notice that you intend to amend.
