The rules have always been that if its addressed correctly and is postmarked by the deadline that its considered to be mailed on time. What about this circumstance causes you to feel that it does not apply? I don't recall any specific instances of original returns mailed on the three year mark, but I have had many amended returns that were, and the postmark date was what mattered, not the date of reciept.
Edit to add: I have just seen where you posted case law on the subject but that is not what I have seen in practice. The amended returns have always been accepted.
I dug a little deeper after thinking about your reply. And I find I need to correct my original answer. You are quite right that rule for a stand alone refund claim (i.e. not one contained in the originally filed return) like in an amended return would get the benefit of the benefit of the postmark rule in IRC § 7502 because under § 6511 the time for timely filing that claim is 3 years after the original return was filed. So an amended return postmarked on 4/15/2019 would be considered timely to get a refund from a 2015 return. The rule in the statute and case law, though, treated the refund claim on an original return differently, as I explained before. The result was a trap for the unwary as the postmark rule works for most filings but not in the case of the late filed original return. There is no logical reason to treat them differently for the purposes of a refund claim. That was simply the result of an anomaly in how the statute was drafted.
It got me thinking, has that problem not ever been addressed? And the answer is that it has. The IRS and Treasury modified the rule by a regulation effective in 2001. It got around the case law by making a distinction between the filing of the return, which under the statute would be treated as filed when the the IRS received it, and the filing of the refund claim, which is treated as filed by the postmark date. In other words, the IRS effectively views the filing of a late original return with a refund on it as the filing of two things: a return and a refund claim. It's a creative solution to the problem. Thus, Treas. Reg. § 301.7502-1(f) provides the following:
(f) Claim for credit or refund on late filed tax return—(1) In general. Generally, an original income tax return may constitute a claim for credit or refund of income tax. See § 301.6402–3(a)(5). Other original tax returns can also be considered claims for credit or refund if the liability disclosed on the return is less than the amount of tax that has been paid. If section 7502 would not apply to a return (but for the operation of paragraph (f)(2) of this section) that is also considered a claim for credit or refund because the envelope that contains the return does not have a postmark dated on or before the due date of the return, section 7502 will apply separately to the claim for credit or refund if—
(i) The date of the postmark on the envelope is within the period that is three years (plus the period of any extension of time to file) from the day the tax is paid or considered paid (see section 6513), and the claim for credit or refund is delivered after this three-year period; and
(ii) The conditions of section 7502 are otherwise met.
(2) Filing date of late filed return. If the conditions of paragraph (f)(1) of this section are met, the late filed return will be deemed filed on the postmark date.
(3) Example. The rules of this paragraph (f) are illustrated by the following example:
Example. (i) Taxpayer A, an individual, mailed his 2001 Form 1040, “U.S. Individual Income Tax Return,” on April 15, 2005, claiming a refund of amounts paid through withholding during 2001. The date of the postmark on the envelope containing the return and claim for refund is April 15, 2005. The return and claim for refund are received by the Internal Revenue Service (IRS) on April 18, 2005. Amounts withheld in 2001 exceeded A's tax liability for 2001 and are treated as paid on April 15, 2002, pursuant to section 6513.
(ii) Even though the date of the postmark on the envelope is after the due date of the return, the claim for refund and the late filed return are treated as filed on the postmark date for purposes of this paragraph (f). Accordingly, the return will be treated as filed on April 15, 2005. In addition, the claim for refund will be treated as timely filed on April 15, 2005. Further, the entire amount of the refund attributable to withholding is allowable as a refund under section 6511(b)(2)(A).
So if the OP responds to the IRS determination by citing the above regulation and proving that the mail was postmarked by April 15 he/she should indeed get his refund not withstanding the earlier case law that would have denied it.
Note that courts have stated that that it is the postmark that matters in determining the date of filing for § 7502, not a receipt or tracking information provided by the post office. So if the IRS can show the postmark was after the 3 year period the OP will lose not withstanding the certified mail receipt. That circumstance is not common as the post office usually postmarks the mail promptly when accepting the certified mail, but on occasion that can be a problem.