They lay it out pretty clearly in the article. What you are describing might be true for a private company, but that same behavior from a military branch of our government is very different.
This is a really interesting area of law that I don't think has been settled.
One could argue that attaching this tracking pixel to an email is similar to attaching a GPS tracker to a vehicle. In United States v Jones in 2012, the supreme court ruled that placing a GPS device on violated the 4th amendment.
> "the Government's installation of a GPS device on a target's vehicle, and its use of that device to monitor the vehicle's movements, constitutes a 'search'"
Regardless of whether it was "well within normal usage of email" or not is kind of irrelevant.
It is also very different coming from the government as opposed to a private institution.
It is also very different to be targeting a news outlet (especially one that has been critical of you!).
I would absolutely challenge you on both points - this is ABSOLUTELY suspicious, and as they pointed out in the article, likely illegal – and I haven't gone crazy mad with paranoia.