I'm far from a conclusion, but here are some of my thoughts based just on initial research.
RR 77-162 involved a 990 and in general is old and had different facts than OP. But its conclusion is
Therefore, under the circumstances described above, the organization's filing of an incomplete return without reasonable cause is a failure to file a return for the purpose of imposing the penalty provided by section 6652(d)(1) of the Code. Because, under section 6652(d)(1), the organization is considered to have failed to file any return at all, the period of limitations on assessment and collection of tax under section 6501(c)(3) has not started.
TAM 9222002, however, points out
While the Service has long taken the position that filing an incomplete return is tantamount to failing to file the return, see e.g ., Rev. Rul. 77-162, 1977-1 C.B. 400, (filing of incomplete F990 constituted failure to file subject to section 6652(d)(1) penalty), this rule is generally inapplicable where the taxpayer has attempted to report, albeit incorrectly, an amount required to be disclosed on a return. The Supreme Court applied this principle in Zellerbach Paper Co. v. Commissioner , 293 U.S. 172 (1934), where in determining whether the statute of limitations on assessment had commenced when the validity of a return was at issue, the Court noted that:
Perfect accuracy or completeness is not necessary to rescue a return from nullity, if it purports to be a return, is sworn to as such, and evinces an honest and genuine endeavor to satisfy the law. This is so though at the time of filing the omissions or inaccuracies are such as to make amendment necessary.
RR 72-161 involved payroll tax returns in 5 situations. Two of the 5 were deemed not valid returns for SOL purposes. Here's why.
Situation (2) is not a valid return for purposes of section 6501 of the Code, since the Service is not able, from that information alone, to determine whether any wages or tips subject to withholding or other compensation was paid and thus the document does not fully set forth the data required to be submitted pursuant to the regulations;
Situation (3) is not a valid return for purposes of section 6501 of the Code, since the Service is not able, from that information alone, to determine whether any tax should have been withheld or whether the $5,000 reported is "other compensation";
Service Center Advice 200304031 involved completely different facts from OP, but its analysis is useful.
In making the determination of whether a given document should be treated as a return for statute of limitation purposes, it is helpful to review the case law on this issue. In an early case addressing what constitutes a return for purposes of the statute of limitations on assessment, the Supreme Court indicated that a "defective" or "incomplete" return may be sufficient to start the running of the period of limitation if it is a specific statement of the items of income, deductions, and credits in compliance with the statutory duty to report information. To have such effect, however, the return must honestly and reasonably be intended as such. Florsheim Bros. Drygoods Co. v. United States , 280 U.S. 453 (1930).
In Zellerbach Paper Co. v. Helvering , 293 U.S. 172 (1934), the taxpayer filed its original income and profits tax return for its fiscal year ending April 30, 1921, in July 1921. Although the Revenue Act of 1921 required taxpayers to file a new or supplemental income and profits tax return if the original return had been prepared pursuant to the provisions of the Revenue Act of 1918 and additional tax was due under the Revenue Act of 1921, the taxpayer did not file a new or supplemental return. When the Commissioner issued a deficiency notice to the taxpayer in May 1928, the taxpayer alleged that the notice was barred because the period of limitations for assessment had expired. The Commissioner argued that the period of limitations for assessment had not begun because the return he received from the taxpayer in July 1921 was a nullity. The Supreme Court disagreed and determined that the period of limitations had expired. The Court concluded that, for purposes of the statutes of limitations,
perfect accuracy or completeness is not necessary to rescue a return from nullity, if it purports to be a return, is sworn to as such, and evinces an honest and genuine endeavor to satisfy the law. This is so even though at the time of filing the omissions or inaccuracies are such as to make amendment necessary.
293 U.S. at 180 (citation omitted).
The most recent Supreme Court reaffirmation of the test articulated in Florsheim and Zellerbach is found in Badaracco v. Commissioner, 464 U.S. 386 (1984). There, the taxpayer filed a return which he conceded was “false or fraudulent with the intent to evade law.” Id. at 393. He later filed a nonfraudulent amended return. The taxpayer argued that the original return, to the extent it was fraudulent, was a nullity for purposes of the statute of limitations. The Court disagreed, noting that the fraudulent original returns
"purported to be returns, were sworn to as such, and appeared on their faces to constitute endeavors to satisfy the law. Although those returns, in fact, were not honest, the holding in Zellerbach does not render them nullities.”
Id. at 397.
The lower courts have subsequently synthesized the criteria enunciated by the Supreme Court into the following four-part test for determining whether a defective or incomplete document is a valid return: "First, there must be sufficient data to calculate tax liability; second, the document must purport to be a return; third, there must be an honest and reasonable attempt to satisfy the requirements of the tax law; and fourth, the taxpayer must execute the return under penalties of perjury." Beard v. Commissioner , 82 T.C. 766, 777 (1984), aff'd per curiam, 793 F.2d 139 (6th Cir. 1986).
This generally accepted formulation of the criteria for determining a valid return is known as the "substantial compliance" standard. If a defective or incomplete document meets the substantial compliance standard, the document is a valid return for purposes of the statute of limitations on assessment and for purposes of determining the failure to file penalty of section 6651(a) of the Code. A document that does not meet the substantial compliance standard is a nullity for purposes of the Code.
Yes, these are old documents and some are not "authorities" for some purposes. And they all precede the 1.2012-2 reg. amendment in 2010. But they seem generally to be useful in analyzing the IRS position on my question.
Plus, and i do see this as pretty significant, the reg. excerpted above is very specific in requiring Schedule UTP in accordance with instructions. It's not a reg. that has been invalidated. It's authoritative and may be a game changer in OP facts.