"But from my reading of Kitces blog, if the beneficiaries never took the full RMD (e.g., never told the acct custodian which stock to sell from a brokerage IRA to raise the cash for the distribution), it would be the estate that owed the penalty."
It seems unlikely that Kitces would have said that since the account becomes maintained for the benefit of the beneficiaries upon the death of the participant and CFR § 1.401(a)(9)-5 Q&A 4 says that this must be distributed to "a beneficiary," implying that it is a beneficiary who fails to complete the RMD not the estate of the decedent. If you can provide a link to the blog post, I'll read it.
It IRS does not seem to aggressively pursue missed RMDs, so an issue is only likely to come up if there is an audit and the audit would provide an opportunity to provide a complete explanation. As long as it can be demonstrated that the remainder of the year-of-death RMD was eventually taken by "a beneficiary" and that there was at least some attempt to request the waiver, the IRS is likely to be satisfied.
Regarding your suggested preparation of Form 5329, I think I would do as you indicated in your second alternative with $500 on line 52, then provide full explanation in the explanation statement.
