It's an insult. They're comparing people with legitimate concerns backed by evidence and precedent to paranoid schizophrenics. They are implicitly saying that people who value privacy are delusional and mentally ill.
This is just picking on an open-source team which already has shown themselves to take user feedback about privacy seriously. If you are so suspect of third parties that any device or application sending any network traffic without previous authorization is of serious concern to you, there's a lot more important and impactful products to voice concern about. Like pretty much any other part of Microsoft.
But I'm sympathetic to Github here. Having users on unpatched software is a bigger risk to them than not having 100% perfect insulation from sending their IP address to Microsoft.
That's not a decision for Github to make. Let the user decide. Perhaps by even presenting them with a dialog on first run that informs them then asks them ti decide.
Somewhere out there (prog21 ?) is an article stating that the one in desperate need of electricity (the computing device) is subject to the one in a position to provide it (the user), and I agree with that sentiment.
I'd even like an IETF-standard-like T-shirt that says 'The user's will MUST be obeyed as faithfully as possible unless prevented by unrecoverable circumstances' or something like that.
Click-through EULAs and dialog boxes are another symptom of the 'elite-developer-itis' our industry can sometimes exude.
Blaming tone is too easy - at this point the Atom team is representing Microsoft, so I'd say the burden is on them to soak up a little snark; especially coming from a user who maybe expects them to behave a bit more like the GitHub of old. Even if they were a small open-source team I would still expect them to directly confront the issue instead of beating around the bush. It's about privacy, and splitting hairs to deny the reporter's reality is a bad look.