What is the program?

There are two different answers to this question, and which one is "correct" depends entirely on the context of who is asking it.

1. It's the code that is specific to this program that sits above the run-time layer (internal view, that most programmers would take).

2. It's the code in the binary that is executed (external view, that most users would take).

The key question does not seem to be "was the proof correct", rather "did the proof cover everything in the program". The answer depends on whether you are looking at it from the perspective of a programmer, or a user. Given the overly strong framing that the article is responding to - highlighting the difference in this way does seem to be useful. The title is correct from the perspective that most users would take.

Yes but, without wishing to be snarky, did you read the article? There is no program as such, in either sense - the announcement from Lean only mentions "a C compression library" (zlib). Not only that, but since we're talking about formal verification, a programmer would likely understand that that is about proving a bounded, specific codebase at source code level, and not operating on a binary along with its associated dependencies (again caveat my limited understanding of these things).

My feeling is that if you told the average non-technical user that some person/organisation had produced a formally verified version of a C compression library, you would likely get a blank look, so I think it's reasonable to assume that both Lean's intended audience, and the audience of the blog post linked here, correspond with number 1. in your list.