No, you cannot put Cynthia's shortfall under Thomas' name. Forms 5329 are individual tax forms, not joint tax forms, so putting it on Thomas' Form 5329 will not give to Cynthia the waiver.
If you cannot get TurboTax to prepare a Form 5329 requesting a waiver for Cynthia because Cynthia received no Forms 1099-R, simplest would be to prepare one manually and include it with your paper tax return filed by mail.
