This makes sense to me since leaving a comment (even a negative one) would be a signal of engagement that would likely boost the likelihood of a given article being/remaining on the front page.
I agree, it's the same principal as spam. You don't reply calling them out as a spammer, as that only signals that they have access to your attention. You blackhole the spam or sender or submit to authorities of services that can help you block it in the future, but you do not engage with the originator.
Spam is the extreme example. What about family or acquaintances who compulsively forward every garbage blog post they come across on whatever their political obsession is? What do you do when they don't respect multiple polite requests to take you off their CC: list? At some point you go, "the hell with seeming disengaged and just letting this trash pass without comment."
I'll happily forfeit my right to remain aloof and to give no signs of engagement if I get annoyed to the point where I'd prefer to go to war.
The rule is not to force you to be a better person by making you consider all comments you see, it's to keep discussion useful and help the site continue to provide a high level of usefulness for all users, including yourself.
In that respect, ignoring, flagging, and shallow dismissals replies are three distinctly different outcomes with different utility to the users of this site.