I’m not sure why SirWired focuses on international borders (point 2) or on foreign citizens who aren’t US citizens or residents (point 5) anyway, since (a) both the TSA procedures at issue, and the Identity Project complaint, relate to domestic travel within the USA, (b) the original article noted that some different treatment at borders is legal (although, again, it still must satisfy specific standards), and (c) the complaint is specifically about discriminatory treatment of dual citizens and green-card holders.

As for why a green-card holder would present a foreign passport as evidence of their identity at a TSA checkpoint: In many cases that’s their only government-issued ID. A green card is not an “identification” card, but is solely evidence of immigration status and lawful presence in the USA. Although, as noted in the article, there are no regulations or statutes requiring ID or specifying what is required, a green card is not ID at all. There’s nothing in the SOP to instruct TSA officers to inquire as to the residency of foreign passport holders, nor does the TSA have any authority to demand answers to such questions.

1) Article 12 of the ICCPR explicitly has an exception for national security. (We could argue about how necessary or effective the measures are, but they aren’t going to be unnecessary enough to win a lawsuit.)
2) You say: “Some discrimination at borders and against foreigners based on national origin may be legal, if reprehensible, under U.S. law (although it may not satisfy the standards for compliance with the ICCPR)” Every nation discriminates against foreign citizens at border crossings. Every. Single. One. (Every international airport I’ve been to has separate lines for different passport holders.) Moreover, Article 12 of the ICCPR is completely silent on border controls for foreign citizens entering a country. It says not a word.
3) I’m having trouble imagining why a dual citizen or green-card holder would choose to present their non-U.S. passport at the security line at a U.S. airport.
4) It is true that discrimination against a dual-citizen or green-card holder is illegal. However, if that citizen or perm. resident chooses to present themselves solely as a non-citizen/perm. resident, additional screening is allowed, legal, and makes sense. (How is the screening officer supposed to know that the citizen/perm. resident is one if they don’t present U.S. ID?) If you were to attempt to get a job, and refused to fill out your I-9 form (the one where you prove your eligibility to work in the U.S.), it would be illegal for the employer to NOT discriminate against you, even if you turn out to be a U.S. citizen. It is little different here.
5) Under law, national origin and national citizenship are two separate things. National origin refers to your place of birth, ancestry, association, etc. (see 29 C.F.R. § 1606.1 as an example), and discrimination for which is certainly illegal. Discrimination based on citizenship (provided you are NOT a U.S. citizen or perm. resident) is perfectly legal under most circumstances.

I’m not saying the procedures work. But they certainly are not illegal.

The TSA does a lot of things wrong. Their procedures are arbitrary and often useless. They routinely violate the rights of travelers. However, uninformed jeremiads like this one are not productive as a means of producing change.