I have a different take on it (perhaps out of wishful thinking).  The (well-respected) author focuses on the mechanics of the refund based on the statutory language of §6428(f)(1).  I would, however, argue that Sec. 2201(d) of the CARES Act is the overarching clause that protects such refunds from offsets:

(d) EXCEPTION FROM REDUCTION OR OFFSET.—Any credit or refund allowed or made to any individual by reason of section 6428 of the Internal Revenue Code of 1986 (as added by this section) or by reason of subsection (c) of this section shall not be—
(1) subject to reduction or offset pursuant to section 3716 or 3720A of title 31, United States Code,
(2) subject to reduction or offset pursuant to subsection (d), (e), or (f) of section 6402 of the Internal Revenue Code of 1986, or H. R. 748—59
(3) reduced or offset by other assessed Federal taxes that would otherwise be subject to levy or collection.

The key is that this subsection refers to "any refund allowed or made to any individual by reason of section 6428".  The term "refund" should be read not as a mechanic of delivery but as one that is defined under §6428(f), particularly subparagraph (2).

The fact this refund is accomplished through a make-believe tax payment should not negate the protection offered here.  After all, §6428(f)(1) alone does not provide sufficient authority to the IRS to issue a refund, without establishing a taxpayer's liability, prior to a return being filed as a claim under §6511 or by means of a substitute return issued by the IRS pursuant to §6020.  Offsetting the advance refund only against outstanding balance on returns filed by taxpayers for 2019 seem to deviate from the intent and plain reading of Sec. 2201(d) of the CARES Act and will create disparate application of §6428 for those who have filed a 2019 return vs those who have not.