Recent green card holders, asylees, and refugees get federal protection, except when a law requires or permits otherwise. The other commenter’s company has a blanket rule of allowing none of these categories. Approximately this got SpaceX into trouble with the DOJ recently.

Some state or local laws offer additional protections beyond federal law, including NYC for all immigration statuses, except as required or allowed by other applicable laws. (So, for example, NYC doesn’t pretend that companies have to hire people who don’t already have employment authorization.)

Not all government contracts require all employees working on the contract to have clearances or be US citizens.

True, but they aren’t allowing recently admitted permanent residents, asylees, and refugees, all of whom have federal protections against immigration status discrimination in employment.

Some places like NYC offer legal protections in this area to all categories of immigration status, of course within what applicable federal and state law requires and allows. Federal law allows preferring citizens over equally equalities noncitizens, requiring employment authorization to already exist, and complying with any specific legal requirements for restricting certain jobs to citizens. NYC law respects all of this. But overall NYC is totally allowed to, and does, add protections beyond federal law.

You are referring to ITAR. Under ITAR, permanent residents are considered US Persons and not subject to export controls. Clearance is a totally different thing that people often confuse with ITAR, which is only granted to US citizens, and though it is possible to grant something somewhat like clearance to non us citizens, it is almost never done.

Edit: Ah I see you are not disagreeing with what I said at all. Apologies, I cannot count the number of times I have seen in reddit and here, where people confuse ITAR with clearance.