The IRS has never provided any specific guidance on this. Your suggestion to have the beneficiary who received the distribution that completed the RMD be the one to file the Form 5329 requesting the waiver seems reasonable.
The estate has nothing to do with this unless the estate is a beneficiary of the IRA (and from the details it seems that the estate is not a beneficiary. Unless the estate is a beneficiary, the estate has no responsibility to receive income from this IRA and no reason to file Form 5329 for this RMD shortfall.
