"I am thinking the only alternative is to due a request for installment payments."

Now you are Mixing Up provisions.

The disaster distribution provision is why you would have three years to Repay the distribution, or to spread the tax hit on the Distribution Amount over three years. Not the entire amount a taxpayer owes to the IRS due to their 1040.

Installment agreements are a type of Settlement negotiation for people who are Broke and cannot pay their tax debt.

You likely could amend the return to show the max of $100,000 as disaster distribution and the remainder is a Partial regular taxable Distribution.

"The return has already been electronic filed and the taxpayer wants to know how to claim tax due over three years."

Well, that horse left the burning barn already and is in the next County!

"I am not sure it can be done due to the fact that the withdrawal was for over $200.000.00 and tax of $34,000 was shown withheld on the 1099R."

The Withholding is already paid in, and is not Refundable. It also isn't Tax Owed on the distribution. It's a forced prepayment.

Are you going to amend their return, then?

Make sure they understand the difference between Tax Balance Owed, and Tax on the $100,000 portion of a Disaster Distribution. You are mixing up provisions that you need to understand to guide your client.